X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 02:51:12 Author: Axel T. Brunger Copyright: 1988-96 (Yale University), 1987 (Harvard University) X-PLOR>! refine.inp -- Clean up the output of dgsa.inp using simulated annealing, X-PLOR>! including Van der Waals and electrostatic forces X-PLOR>! Dave Schweisguth , 21 Jul 1996 X-PLOR>! Derived from nmr/refine_gentle.inp X-PLOR> X-PLOR>evaluate ($t=300) ! Temperature for constant-temperature MD EVALUATE: symbol $T set to 300.000 (real) X-PLOR>evaluate ($steps=40000) ! Number of steps of constant-temperature MD EVALUATE: symbol $STEPS set to 40000.0 (real) X-PLOR>evaluate ($timestep=0.0005) ! Time of each MD step EVALUATE: symbol $TIMESTEP set to 0.500000E-03 (real) X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use 'xplor -s' ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/xplor.seed opened. SEED=52488.7803039551 SET> end ! Use 'xplor -s' X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 96000) NBOND= 728(MAXB= 96000) NTHETA= 1299(MAXT= 144000) NGRP= 218(MAXGRP= 96000) NPHI= 0(MAXP= 180000) NIMPHI= 461(MAXIMP= 96000) NDON= 68(MAXPAD= 24000) NACC= 105(MAXPAD= 24000) NNB= 63(MAXNB= 18000) NOE: allocating space for 1000 restraints. XREFIN: allocating space for 300 assignments. X-PLOR> X-PLOR>noe ! Parameters for NOE effective energy term. NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1 NOE> sqexponent * 2 NOE> scale * 100 ! Constant NOE scale throughout the protocol. NOE>end X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> ctonnb=9.5 NBDSET> ctofnb=10.5 NBDSET> cutnb=11.5 NBDSET> tolerance=0.5 NBDSET> rdie NBDSET> switch NBDSET> vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR>restraints dihedral scale=800 end X-PLOR> X-PLOR>coordinates @dgsa.pdb ! END in PDB file ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/dgsa.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dgsa.pdb" COOR>REMARK 5 DATE:16-Aug-96 18:21:26 created by user: COOR>ATOM 1 P GUA A 1 -6.729 12.277 -0.573 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -5.270 12.237 -0.851 1.00 0.00 A X-PLOR> ! END in PDB file X-PLOR> X-PLOR>flags exclude * include bond angl dihe impr vdw elec noe cdih plan end X-PLOR> X-PLOR>! Intial minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2090 exclusions and 1650 interactions(1-4) %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H5''" only 1.36 A apart %atoms "A -11 -ADE -O5' " and "A -12 -URI -O5' " only 0.49 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64391 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H5''" only 1.36 A apart %atoms "A -11 -ADE -O5' " and "A -12 -URI -H3' " only 1.02 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64373 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H5''" only 1.36 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64373 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H5''" only 1.50 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -H5' " only 1.41 A apart NBONDS: found 64382 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =1843.880 grad(E)=13.707 E(BOND)=326.916 E(ANGL)=833.782 | | E(DIHE)=0.000 E(IMPR)=35.728 E(VDW )=385.494 E(ELEC)=-83.140 | | E(CDIH)=176.458 E(NOE )=158.391 E(PLAN)=10.251 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.50 A apart NBONDS: found 64409 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64467 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =1467.074 grad(E)=13.829 E(BOND)=270.110 E(ANGL)=768.718 | | E(DIHE)=0.000 E(IMPR)=34.039 E(VDW )=230.215 E(ELEC)=-90.871 | | E(CDIH)=79.594 E(NOE )=163.825 E(PLAN)=11.444 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64491 intra-atom interactions --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =1307.016 grad(E)=8.335 E(BOND)=207.847 E(ANGL)=694.519 | | E(DIHE)=0.000 E(IMPR)=36.676 E(VDW )=202.346 E(ELEC)=-93.010 | | E(CDIH)=60.019 E(NOE )=186.539 E(PLAN)=12.081 | ------------------------------------------------------------------------------- NBONDS: found 64553 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =1225.006 grad(E)=9.739 E(BOND)=181.256 E(ANGL)=698.127 | | E(DIHE)=0.000 E(IMPR)=37.376 E(VDW )=107.277 E(ELEC)=-98.316 | | E(CDIH)=77.557 E(NOE )=209.535 E(PLAN)=12.193 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 64614 intra-atom interactions --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =1171.269 grad(E)=4.245 E(BOND)=157.133 E(ANGL)=697.508 | | E(DIHE)=0.000 E(IMPR)=44.235 E(VDW )=61.315 E(ELEC)=-102.784 | | E(CDIH)=70.357 E(NOE )=231.007 E(PLAN)=12.497 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =1148.837 grad(E)=3.117 E(BOND)=155.906 E(ANGL)=689.163 | | E(DIHE)=0.000 E(IMPR)=42.015 E(VDW )=41.809 E(ELEC)=-104.280 | | E(CDIH)=62.910 E(NOE )=248.889 E(PLAN)=12.426 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =1136.975 grad(E)=2.969 E(BOND)=154.519 E(ANGL)=674.849 | | E(DIHE)=0.000 E(IMPR)=43.703 E(VDW )=43.287 E(ELEC)=-105.628 | | E(CDIH)=58.701 E(NOE )=255.244 E(PLAN)=12.299 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =1125.949 grad(E)=3.283 E(BOND)=152.049 E(ANGL)=670.116 | | E(DIHE)=0.000 E(IMPR)=45.614 E(VDW )=42.260 E(ELEC)=-108.087 | | E(CDIH)=59.932 E(NOE )=251.740 E(PLAN)=12.325 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Constant temperature SA X-PLOR> X-PLOR>vector do (fbeta=100) (all) ! Coupling to heat bath. SELRPN: 677 atoms have been selected out of 677 X-PLOR>dynamics verlet DYNAmics> iasvel=maxwell DYNAmics> firsttemperature=$t DYNAmics> tbath=$t DYNAmics> tcoup=true DYNAmics> nstep=$steps DYNAmics> timestep=$timestep DYNAmics> nprint=250 DYNAmics> iprfrq=2500 DYNAmics> trajectory=refine.tra DYNAmics> nsavc=200 ! Save trajectory to file. DYNAmics>end ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.tra opened. DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 236117819. ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.07349 0.03457 -0.00585 velocity [A/ps] : -0.02046 -0.24526 -0.20167 ang. mom. [amu A/ps] : -4365.03703 -26167.22695 -10782.27520 kin. ener. [Kcal/mol] : 0.81606 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.07349 0.03457 -0.00585 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=1725.810 E(kin)=599.862 temperature=297.257 | | Etotal =1125.949 grad(E)=3.283 E(BOND)=152.049 E(ANGL)=670.116 | | E(DIHE)=0.000 E(IMPR)=45.614 E(VDW )=42.260 E(ELEC)=-108.087 | | E(CDIH)=59.932 E(NOE )=251.740 E(PLAN)=12.325 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart NBONDS: found 64941 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 64902 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart NBONDS: found 64963 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.45 A apart NBONDS: found 64992 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.49 A apart NBONDS: found 65077 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 65206 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart NBONDS: found 65293 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 65439 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart NBONDS: found 65552 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=2252.522 E(kin)=563.117 temperature=279.048 | | Etotal =1689.405 grad(E)=70.367 E(BOND)=334.168 E(ANGL)=918.889 | | E(DIHE)=0.000 E(IMPR)=132.670 E(VDW )=95.452 E(ELEC)=-118.981 | | E(CDIH)=45.008 E(NOE )=268.691 E(PLAN)=13.508 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.44 A apart NBONDS: found 65657 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.50 A apart NBONDS: found 65760 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.43 A apart NBONDS: found 65915 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.46 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.49 A apart NBONDS: found 65992 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.30 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 66068 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.33 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.48 A apart NBONDS: found 66105 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.26 A apart %atoms "A -11 -ADE -O4' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.45 A apart NBONDS: found 66141 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.30 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.47 A apart NBONDS: found 66203 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.49 A apart NBONDS: found 66227 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.31 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.49 A apart NBONDS: found 66228 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=2174.685 E(kin)=598.538 temperature=296.601 | | Etotal =1576.147 grad(E)=65.342 E(BOND)=349.703 E(ANGL)=804.784 | | E(DIHE)=0.000 E(IMPR)=106.855 E(VDW )=42.860 E(ELEC)=-128.314 | | E(CDIH)=51.583 E(NOE )=331.817 E(PLAN)=16.859 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.30 A apart NBONDS: found 66306 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.34 A apart NBONDS: found 66255 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.30 A apart NBONDS: found 66335 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.36 A apart NBONDS: found 66381 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart NBONDS: found 66369 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart NBONDS: found 66364 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart NBONDS: found 66377 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart NBONDS: found 66430 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.31 A apart NBONDS: found 66448 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.31 A apart NBONDS: found 66450 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=2095.038 E(kin)=644.252 temperature=319.254 | | Etotal =1450.786 grad(E)=57.261 E(BOND)=283.663 E(ANGL)=759.035 | | E(DIHE)=0.000 E(IMPR)=112.337 E(VDW )=4.696 E(ELEC)=-132.833 | | E(CDIH)=48.848 E(NOE )=360.745 E(PLAN)=14.296 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.34 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.45 A apart NBONDS: found 66460 intra-atom interactions NBONDS: found 66517 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66567 intra-atom interactions %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.44 A apart %atoms "A -11 -ADE -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66669 intra-atom interactions %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.46 A apart %atoms "A -11 -ADE -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66718 intra-atom interactions %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.47 A apart %atoms "A -11 -ADE -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66711 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66709 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.46 A apart %atoms "A -10 -CYT -H2' " and "A -12 -URI -H5''" only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66651 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart NBONDS: found 66647 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=1916.212 E(kin)=599.936 temperature=297.293 | | Etotal =1316.276 grad(E)=57.311 E(BOND)=266.316 E(ANGL)=640.054 | | E(DIHE)=0.000 E(IMPR)=121.194 E(VDW )=1.742 E(ELEC)=-124.342 | | E(CDIH)=13.531 E(NOE )=383.304 E(PLAN)=14.478 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H3' " only 1.48 A apart NBONDS: found 66567 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -12 -URI -H5''" only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66416 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66347 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66266 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 66149 intra-atom interactions %atoms "A -11 -ADE -H8 " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 66057 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65969 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65800 intra-atom interactions %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65592 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=1954.640 E(kin)=620.823 temperature=307.644 | | Etotal =1333.817 grad(E)=55.853 E(BOND)=257.596 E(ANGL)=670.398 | | E(DIHE)=0.000 E(IMPR)=131.343 E(VDW )=-13.477 E(ELEC)=-118.728 | | E(CDIH)=26.644 E(NOE )=366.048 E(PLAN)=13.993 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65438 intra-atom interactions %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.43 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65424 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.45 A apart %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65367 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.48 A apart %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.35 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65323 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.42 A apart %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.37 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65276 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.44 A apart %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.44 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart NBONDS: found 65220 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.44 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65266 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.47 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H42 " and "A -14 -ADE -H62 " only 1.47 A apart NBONDS: found 65260 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.46 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.30 A apart NBONDS: found 65261 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=1838.167 E(kin)=607.578 temperature=301.080 | | Etotal =1230.590 grad(E)=55.571 E(BOND)=221.382 E(ANGL)=618.896 | | E(DIHE)=0.000 E(IMPR)=155.537 E(VDW )=-12.633 E(ELEC)=-133.789 | | E(CDIH)=16.053 E(NOE )=350.673 E(PLAN)=14.472 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.48 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.28 A apart NBONDS: found 65265 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.27 A apart NBONDS: found 65241 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.31 A apart NBONDS: found 65247 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.30 A apart NBONDS: found 65268 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.22 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.49 A apart NBONDS: found 65304 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.22 A apart NBONDS: found 65328 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.31 A apart NBONDS: found 65369 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.29 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.48 A apart NBONDS: found 65383 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.27 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 65381 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.49 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.28 A apart %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 65405 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.43 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65458 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65429 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart NBONDS: found 65443 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 65476 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=1754.374 E(kin)=598.370 temperature=296.518 | | Etotal =1156.003 grad(E)=52.237 E(BOND)=198.165 E(ANGL)=530.884 | | E(DIHE)=0.000 E(IMPR)=117.200 E(VDW )=-20.018 E(ELEC)=-127.537 | | E(CDIH)=25.943 E(NOE )=412.188 E(PLAN)=19.179 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H1' " and "A -13 -ADE -H61 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 65485 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65491 intra-atom interactions %atoms "A -9 -URI -O3' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.22 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.44 A apart NBONDS: found 65516 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.23 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.45 A apart NBONDS: found 65534 intra-atom interactions %atoms "A -9 -URI -O3' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.24 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65556 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.22 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65510 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.26 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65517 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.26 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65552 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65535 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65553 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 65568 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65597 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.30 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65587 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.23 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65618 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.26 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65648 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -10 -CYT -O2 " and "A -13 -ADE -H61 " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65730 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=1749.915 E(kin)=622.864 temperature=308.655 | | Etotal =1127.052 grad(E)=53.919 E(BOND)=167.940 E(ANGL)=520.534 | | E(DIHE)=0.000 E(IMPR)=156.134 E(VDW )=-46.194 E(ELEC)=-116.643 | | E(CDIH)=21.218 E(NOE )=412.667 E(PLAN)=11.396 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -10 -CYT -O2 " and "A -13 -ADE -H61 " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.46 A apart NBONDS: found 65793 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2 " and "A -13 -ADE -H61 " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65800 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -O2 " and "A -13 -ADE -H61 " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65821 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O2 " and "A -13 -ADE -H61 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 65829 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.49 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65863 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65945 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.27 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 65971 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.33 A apart NBONDS: found 65951 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.27 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65932 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.32 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65897 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=1700.746 E(kin)=614.105 temperature=304.315 | | Etotal =1086.641 grad(E)=52.064 E(BOND)=189.940 E(ANGL)=519.054 | | E(DIHE)=0.000 E(IMPR)=144.699 E(VDW )=-78.590 E(ELEC)=-118.181 | | E(CDIH)=17.647 E(NOE )=399.571 E(PLAN)=12.499 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65848 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65851 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65855 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H4' " only 1.47 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -11 -ADE -H61 " and "A -13 -ADE -H5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65813 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H4' " only 1.50 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -11 -ADE -H61 " and "A -13 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65773 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65731 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65652 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.38 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65602 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65504 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65435 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65358 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65364 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=1679.407 E(kin)=596.965 temperature=295.821 | | Etotal =1082.442 grad(E)=52.327 E(BOND)=169.946 E(ANGL)=505.801 | | E(DIHE)=0.000 E(IMPR)=128.710 E(VDW )=-48.922 E(ELEC)=-121.014 | | E(CDIH)=26.639 E(NOE )=410.217 E(PLAN)=11.065 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1938.168 E(kin)=605.722 temperature=300.161 | | Etotal =1332.446 grad(E)=57.433 E(BOND)=250.307 E(ANGL)=678.312 | | E(DIHE)=0.000 E(IMPR)=125.423 E(VDW )=1.086 E(ELEC)=-124.875 | | E(CDIH)=34.487 E(NOE )=352.258 E(PLAN)=15.446 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=198.803 E(kin)=20.941 temperature=10.377 | | Etotal =199.934 grad(E)=4.990 E(BOND)=52.515 E(ANGL)=131.997 | | E(DIHE)=0.000 E(IMPR)=16.646 E(VDW )=44.845 E(ELEC)=7.057 | | E(CDIH)=16.159 E(NOE )=45.777 E(PLAN)=2.613 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65306 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -11 -ADE -H61 " and "A -13 -ADE -H5''" only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65288 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65262 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65288 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65318 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65350 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65381 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H4' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.31 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65442 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65440 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65459 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65466 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65425 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=1656.055 E(kin)=609.548 temperature=302.057 | | Etotal =1046.507 grad(E)=49.282 E(BOND)=174.416 E(ANGL)=519.363 | | E(DIHE)=0.000 E(IMPR)=109.555 E(VDW )=-21.620 E(ELEC)=-129.700 | | E(CDIH)=23.312 E(NOE )=354.179 E(PLAN)=17.003 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 65393 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 65263 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 65141 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 65126 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65112 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart NBONDS: found 65080 intra-atom interactions %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.48 A apart NBONDS: found 65053 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.45 A apart NBONDS: found 65066 intra-atom interactions %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 65057 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 65036 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 64981 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=1731.688 E(kin)=623.455 temperature=308.948 | | Etotal =1108.233 grad(E)=51.890 E(BOND)=207.231 E(ANGL)=554.280 | | E(DIHE)=0.000 E(IMPR)=127.851 E(VDW )=-48.393 E(ELEC)=-134.119 | | E(CDIH)=22.437 E(NOE )=352.259 E(PLAN)=26.685 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64948 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64934 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64869 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.32 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64783 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.46 A apart NBONDS: found 64717 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64646 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64609 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H5' " only 1.49 A apart NBONDS: found 64583 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64585 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 64582 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.28 A apart NBONDS: found 64542 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64538 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=1718.650 E(kin)=618.588 temperature=306.536 | | Etotal =1100.062 grad(E)=52.682 E(BOND)=200.911 E(ANGL)=496.669 | | E(DIHE)=0.000 E(IMPR)=108.797 E(VDW )=-47.667 E(ELEC)=-132.179 | | E(CDIH)=28.865 E(NOE )=424.805 E(PLAN)=19.861 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -N3 " and "A -13 -ADE -H61 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 64531 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -N3 " and "A -13 -ADE -H61 " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64530 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -N3 " and "A -13 -ADE -H61 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 64539 intra-atom interactions %atoms "A -10 -CYT -N3 " and "A -13 -ADE -H61 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64497 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64481 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 64426 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 64386 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64342 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64290 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64187 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.36 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 64112 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 64028 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.36 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64010 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.33 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 63978 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.26 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63982 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=1774.177 E(kin)=586.007 temperature=290.391 | | Etotal =1188.170 grad(E)=54.769 E(BOND)=237.503 E(ANGL)=568.217 | | E(DIHE)=0.000 E(IMPR)=111.374 E(VDW )=-73.974 E(ELEC)=-123.177 | | E(CDIH)=28.381 E(NOE )=421.553 E(PLAN)=18.293 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.34 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63986 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.34 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63994 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63949 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 63984 intra-atom interactions NBONDS: found 64111 intra-atom interactions NBONDS: found 64134 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64157 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64111 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=1767.516 E(kin)=607.539 temperature=301.061 | | Etotal =1159.978 grad(E)=55.116 E(BOND)=220.198 E(ANGL)=510.983 | | E(DIHE)=0.000 E(IMPR)=121.903 E(VDW )=-37.633 E(ELEC)=-123.530 | | E(CDIH)=29.011 E(NOE )=415.037 E(PLAN)=24.010 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart NBONDS: found 64022 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.31 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63954 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63831 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63739 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63655 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63567 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -11 -ADE -H4' " and "A -11 -ADE -HO2'" only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63521 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.44 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 63416 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63330 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63218 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=1786.415 E(kin)=610.288 temperature=302.423 | | Etotal =1176.127 grad(E)=54.811 E(BOND)=221.441 E(ANGL)=540.855 | | E(DIHE)=0.000 E(IMPR)=135.880 E(VDW )=-39.221 E(ELEC)=-121.718 | | E(CDIH)=27.064 E(NOE )=383.920 E(PLAN)=27.905 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63170 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 63139 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63174 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63239 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63358 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63424 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63445 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63469 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63496 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63543 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=1737.685 E(kin)=597.520 temperature=296.096 | | Etotal =1140.165 grad(E)=55.508 E(BOND)=215.996 E(ANGL)=536.084 | | E(DIHE)=0.000 E(IMPR)=111.570 E(VDW )=-46.184 E(ELEC)=-116.692 | | E(CDIH)=20.916 E(NOE )=401.034 E(PLAN)=17.441 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.29 A apart NBONDS: found 63579 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.29 A apart NBONDS: found 63563 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63563 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63541 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 63518 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63469 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63430 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63478 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.48 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 63441 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.48 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 63424 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.44 A apart %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.35 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 63426 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.42 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 63419 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=1747.010 E(kin)=612.476 temperature=303.507 | | Etotal =1134.534 grad(E)=55.296 E(BOND)=214.623 E(ANGL)=534.060 | | E(DIHE)=0.000 E(IMPR)=109.863 E(VDW )=-50.753 E(ELEC)=-114.134 | | E(CDIH)=32.763 E(NOE )=388.830 E(PLAN)=19.283 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.49 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63404 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63432 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63474 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.29 A apart NBONDS: found 63558 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63603 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -12 -URI -H2' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.44 A apart NBONDS: found 63666 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63740 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63877 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63858 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63877 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63868 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=1696.580 E(kin)=611.625 temperature=303.086 | | Etotal =1084.955 grad(E)=54.495 E(BOND)=200.850 E(ANGL)=516.386 | | E(DIHE)=0.000 E(IMPR)=121.064 E(VDW )=-64.390 E(ELEC)=-127.751 | | E(CDIH)=20.280 E(NOE )=396.458 E(PLAN)=22.057 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63899 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63892 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63893 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 63923 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.28 A apart NBONDS: found 64001 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64026 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64090 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64233 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64226 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64279 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=1666.068 E(kin)=598.860 temperature=296.760 | | Etotal =1067.208 grad(E)=55.996 E(BOND)=184.661 E(ANGL)=542.403 | | E(DIHE)=0.000 E(IMPR)=119.005 E(VDW )=-45.630 E(ELEC)=-131.345 | | E(CDIH)=21.872 E(NOE )=357.637 E(PLAN)=18.605 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1735.883 E(kin)=605.482 temperature=300.042 | | Etotal =1130.401 grad(E)=54.322 E(BOND)=204.063 E(ANGL)=541.665 | | E(DIHE)=0.000 E(IMPR)=122.677 E(VDW )=-50.132 E(ELEC)=-124.993 | | E(CDIH)=24.049 E(NOE )=392.291 E(PLAN)=20.780 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=36.229 E(kin)=11.367 temperature=5.633 | | Etotal =37.809 grad(E)=1.859 E(BOND)=13.244 E(ANGL)=23.546 | | E(DIHE)=0.000 E(IMPR)=12.278 E(VDW )=18.105 E(ELEC)=6.376 | | E(CDIH)=6.110 E(NOE )=25.296 E(PLAN)=3.964 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=1837.026 E(kin)=605.602 temperature=300.101 | | Etotal =1231.423 grad(E)=55.877 E(BOND)=227.185 E(ANGL)=609.989 | | E(DIHE)=0.000 E(IMPR)=124.050 E(VDW )=-24.523 E(ELEC)=-124.934 | | E(CDIH)=29.268 E(NOE )=372.275 E(PLAN)=18.113 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=175.064 E(kin)=16.849 temperature=8.349 | | Etotal =175.804 grad(E)=4.074 E(BOND)=44.735 E(ANGL)=116.863 | | E(DIHE)=0.000 E(IMPR)=14.690 E(VDW )=42.723 E(ELEC)=6.725 | | E(CDIH)=13.284 E(NOE )=42.052 E(PLAN)=4.287 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64342 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart NBONDS: found 64421 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64444 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64492 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64601 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64688 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64734 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64766 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64845 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=1682.038 E(kin)=626.837 temperature=310.624 | | Etotal =1055.201 grad(E)=56.191 E(BOND)=212.091 E(ANGL)=505.423 | | E(DIHE)=0.000 E(IMPR)=114.102 E(VDW )=-52.234 E(ELEC)=-134.212 | | E(CDIH)=29.200 E(NOE )=358.518 E(PLAN)=22.313 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 64916 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 64974 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64974 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64985 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65014 intra-atom interactions NBONDS: found 64989 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65015 intra-atom interactions NBONDS: found 65042 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 65034 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.46 A apart %atoms "A -10 -CYT -HO2'" and "A -12 -URI -H2' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65014 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 65035 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65087 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.31 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.30 A apart NBONDS: found 65089 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=1694.489 E(kin)=603.981 temperature=299.298 | | Etotal =1090.509 grad(E)=57.181 E(BOND)=196.427 E(ANGL)=500.488 | | E(DIHE)=0.000 E(IMPR)=122.285 E(VDW )=-20.372 E(ELEC)=-125.221 | | E(CDIH)=16.376 E(NOE )=380.811 E(PLAN)=19.715 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.28 A apart NBONDS: found 65101 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.32 A apart NBONDS: found 65100 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.28 A apart NBONDS: found 65178 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.24 A apart NBONDS: found 65191 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.32 A apart NBONDS: found 65267 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65324 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -9 -URI -O3' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65357 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart NBONDS: found 65375 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -12 -URI -H2' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.31 A apart NBONDS: found 65442 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.26 A apart NBONDS: found 65517 intra-atom interactions %atoms "A -9 -URI -O3' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart NBONDS: found 65532 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65606 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65581 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65646 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=1727.979 E(kin)=596.652 temperature=295.666 | | Etotal =1131.327 grad(E)=56.542 E(BOND)=229.145 E(ANGL)=526.570 | | E(DIHE)=0.000 E(IMPR)=141.593 E(VDW )=-61.617 E(ELEC)=-129.580 | | E(CDIH)=24.627 E(NOE )=381.447 E(PLAN)=19.142 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65621 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65695 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65758 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65763 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65787 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65828 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65846 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65839 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 65808 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 65821 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 65850 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65921 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=1769.928 E(kin)=606.779 temperature=300.685 | | Etotal =1163.148 grad(E)=58.222 E(BOND)=212.667 E(ANGL)=581.433 | | E(DIHE)=0.000 E(IMPR)=145.041 E(VDW )=-53.727 E(ELEC)=-124.747 | | E(CDIH)=32.134 E(NOE )=359.080 E(PLAN)=11.268 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 65966 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.48 A apart NBONDS: found 65986 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.48 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.46 A apart NBONDS: found 65985 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.42 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 66030 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.45 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 66029 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.47 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 66095 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.50 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart NBONDS: found 66206 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66279 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 66353 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 66406 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66437 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66439 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=1777.276 E(kin)=625.207 temperature=309.816 | | Etotal =1152.069 grad(E)=57.512 E(BOND)=229.469 E(ANGL)=584.024 | | E(DIHE)=0.000 E(IMPR)=126.296 E(VDW )=-57.921 E(ELEC)=-124.360 | | E(CDIH)=9.921 E(NOE )=370.171 E(PLAN)=14.469 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 66469 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 66549 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 66594 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 66622 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 66678 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.36 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 66726 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 66734 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 66815 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 66860 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66895 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66926 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66965 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 67031 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 67078 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=1809.089 E(kin)=602.390 temperature=298.510 | | Etotal =1206.698 grad(E)=58.423 E(BOND)=232.430 E(ANGL)=544.337 | | E(DIHE)=0.000 E(IMPR)=127.634 E(VDW )=-25.227 E(ELEC)=-120.566 | | E(CDIH)=22.518 E(NOE )=412.292 E(PLAN)=13.279 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66995 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66953 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66887 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.48 A apart %atoms "A -9 -URI -O3' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66908 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66875 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66819 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 66786 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart NBONDS: found 66769 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66719 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66690 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 66602 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66549 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=1754.132 E(kin)=605.053 temperature=299.829 | | Etotal =1149.079 grad(E)=58.084 E(BOND)=224.363 E(ANGL)=531.154 | | E(DIHE)=0.000 E(IMPR)=130.926 E(VDW )=-43.340 E(ELEC)=-120.259 | | E(CDIH)=18.165 E(NOE )=390.446 E(PLAN)=17.624 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66510 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66450 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66390 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66371 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 66435 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 66431 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 66453 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.32 A apart NBONDS: found 66465 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.36 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 66445 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.36 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66497 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=1730.039 E(kin)=593.935 temperature=294.320 | | Etotal =1136.103 grad(E)=58.195 E(BOND)=228.213 E(ANGL)=539.853 | | E(DIHE)=0.000 E(IMPR)=122.569 E(VDW )=-35.198 E(ELEC)=-125.205 | | E(CDIH)=28.626 E(NOE )=363.936 E(PLAN)=13.310 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66494 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66371 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66308 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66238 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66126 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65985 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65840 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart NBONDS: found 65755 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65456 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=1727.185 E(kin)=609.343 temperature=301.955 | | Etotal =1117.842 grad(E)=56.544 E(BOND)=211.252 E(ANGL)=523.782 | | E(DIHE)=0.000 E(IMPR)=124.660 E(VDW )=-55.582 E(ELEC)=-127.680 | | E(CDIH)=16.141 E(NOE )=406.405 E(PLAN)=18.864 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65256 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65101 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart NBONDS: found 65030 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 64947 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64910 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64822 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 64781 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64755 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.33 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64780 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=1709.378 E(kin)=596.318 temperature=295.501 | | Etotal =1113.059 grad(E)=56.899 E(BOND)=231.580 E(ANGL)=543.879 | | E(DIHE)=0.000 E(IMPR)=130.029 E(VDW )=-67.282 E(ELEC)=-135.033 | | E(CDIH)=12.659 E(NOE )=375.078 E(PLAN)=22.150 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1739.973 E(kin)=605.266 temperature=299.935 | | Etotal =1134.707 grad(E)=57.213 E(BOND)=218.391 E(ANGL)=543.663 | | E(DIHE)=0.000 E(IMPR)=128.013 E(VDW )=-55.281 E(ELEC)=-126.275 | | E(CDIH)=23.611 E(NOE )=385.199 E(PLAN)=17.385 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=39.879 E(kin)=11.544 temperature=5.720 | | Etotal =41.080 grad(E)=1.662 E(BOND)=13.484 E(ANGL)=25.628 | | E(DIHE)=0.000 E(IMPR)=11.763 E(VDW )=16.357 E(ELEC)=4.762 | | E(CDIH)=5.335 E(NOE )=21.467 E(PLAN)=3.029 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=1804.675 E(kin)=605.490 temperature=300.046 | | Etotal =1199.185 grad(E)=56.323 E(BOND)=224.254 E(ANGL)=587.880 | | E(DIHE)=0.000 E(IMPR)=125.371 E(VDW )=-34.776 E(ELEC)=-125.381 | | E(CDIH)=27.383 E(NOE )=376.583 E(PLAN)=17.870 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=151.838 E(kin)=15.287 temperature=7.575 | | Etotal =152.466 grad(E)=3.519 E(BOND)=37.576 E(ANGL)=101.494 | | E(DIHE)=0.000 E(IMPR)=13.910 E(VDW )=38.939 E(ELEC)=6.173 | | E(CDIH)=11.586 E(NOE )=37.009 E(PLAN)=3.928 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.28 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64738 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 64713 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.28 A apart NBONDS: found 64797 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 64769 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64751 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64758 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64699 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64730 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=1691.376 E(kin)=595.816 temperature=295.252 | | Etotal =1095.560 grad(E)=56.565 E(BOND)=229.161 E(ANGL)=505.510 | | E(DIHE)=0.000 E(IMPR)=121.201 E(VDW )=-51.786 E(ELEC)=-123.381 | | E(CDIH)=17.568 E(NOE )=375.337 E(PLAN)=21.949 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64706 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64697 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 64597 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 64621 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 64577 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 64506 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64431 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64351 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 64338 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64271 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=1710.308 E(kin)=610.526 temperature=302.541 | | Etotal =1099.782 grad(E)=58.047 E(BOND)=208.751 E(ANGL)=533.212 | | E(DIHE)=0.000 E(IMPR)=120.220 E(VDW )=-49.762 E(ELEC)=-136.504 | | E(CDIH)=23.487 E(NOE )=379.343 E(PLAN)=21.035 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64271 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 64258 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 64174 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 64037 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63912 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 63850 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63778 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63790 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63763 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63762 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=1729.746 E(kin)=611.631 temperature=303.089 | | Etotal =1118.115 grad(E)=57.825 E(BOND)=223.025 E(ANGL)=519.004 | | E(DIHE)=0.000 E(IMPR)=122.114 E(VDW )=-50.983 E(ELEC)=-127.679 | | E(CDIH)=24.130 E(NOE )=389.675 E(PLAN)=18.829 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63741 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 63698 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63712 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63743 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63712 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63694 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63705 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63693 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63682 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63682 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H8 " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63689 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.30 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63706 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=1776.927 E(kin)=607.218 temperature=300.902 | | Etotal =1169.709 grad(E)=59.237 E(BOND)=227.578 E(ANGL)=548.895 | | E(DIHE)=0.000 E(IMPR)=151.348 E(VDW )=-70.659 E(ELEC)=-127.108 | | E(CDIH)=27.866 E(NOE )=389.554 E(PLAN)=22.236 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63664 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63664 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63614 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63629 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63658 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63661 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63668 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63677 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63671 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63674 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63750 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.39 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63818 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.33 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63888 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=1744.083 E(kin)=600.540 temperature=297.593 | | Etotal =1143.543 grad(E)=60.938 E(BOND)=240.078 E(ANGL)=545.407 | | E(DIHE)=0.000 E(IMPR)=137.977 E(VDW )=-69.260 E(ELEC)=-120.993 | | E(CDIH)=14.819 E(NOE )=374.982 E(PLAN)=20.532 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.35 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63999 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 64068 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 64066 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 64122 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64148 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64282 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64348 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 64372 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 64418 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.29 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64467 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.31 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64479 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.28 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64480 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=1783.376 E(kin)=596.296 temperature=295.490 | | Etotal =1187.080 grad(E)=61.770 E(BOND)=234.271 E(ANGL)=586.440 | | E(DIHE)=0.000 E(IMPR)=122.746 E(VDW )=-79.483 E(ELEC)=-127.176 | | E(CDIH)=22.421 E(NOE )=404.512 E(PLAN)=23.348 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.35 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64465 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.30 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 64531 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64573 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.33 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64593 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64639 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.30 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64683 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.33 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64780 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.33 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64832 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.42 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64879 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.17 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64954 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=1784.339 E(kin)=592.824 temperature=293.769 | | Etotal =1191.515 grad(E)=59.458 E(BOND)=258.044 E(ANGL)=554.075 | | E(DIHE)=0.000 E(IMPR)=132.739 E(VDW )=-78.596 E(ELEC)=-128.107 | | E(CDIH)=22.776 E(NOE )=409.762 E(PLAN)=20.823 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65005 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.47 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65049 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 65082 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 65110 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65128 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65114 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65157 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 65163 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 65176 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 65135 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 65079 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=1761.212 E(kin)=603.239 temperature=298.930 | | Etotal =1157.973 grad(E)=60.568 E(BOND)=227.142 E(ANGL)=570.208 | | E(DIHE)=0.000 E(IMPR)=131.914 E(VDW )=-55.258 E(ELEC)=-117.737 | | E(CDIH)=22.329 E(NOE )=358.714 E(PLAN)=20.662 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 65039 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64969 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64960 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64938 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64940 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 64966 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64962 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -10 -CYT -H41 " only 1.50 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65001 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65011 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 65032 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65017 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65000 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=1740.677 E(kin)=597.415 temperature=296.044 | | Etotal =1143.262 grad(E)=60.936 E(BOND)=223.699 E(ANGL)=555.180 | | E(DIHE)=0.000 E(IMPR)=131.723 E(VDW )=-61.536 E(ELEC)=-130.307 | | E(CDIH)=25.888 E(NOE )=376.593 E(PLAN)=22.023 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64960 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 64916 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64917 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64903 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64855 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64844 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 64876 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64861 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64865 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 64863 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64849 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=1728.933 E(kin)=596.329 temperature=295.506 | | Etotal =1132.605 grad(E)=59.575 E(BOND)=218.431 E(ANGL)=558.586 | | E(DIHE)=0.000 E(IMPR)=118.436 E(VDW )=-61.381 E(ELEC)=-124.035 | | E(CDIH)=31.982 E(NOE )=370.843 E(PLAN)=19.742 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1744.978 E(kin)=605.373 temperature=299.988 | | Etotal =1139.605 grad(E)=59.433 E(BOND)=228.723 E(ANGL)=545.528 | | E(DIHE)=0.000 E(IMPR)=127.536 E(VDW )=-59.592 E(ELEC)=-126.996 | | E(CDIH)=23.052 E(NOE )=381.214 E(PLAN)=20.140 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=33.798 E(kin)=11.510 temperature=5.704 | | Etotal =35.432 grad(E)=1.646 E(BOND)=13.840 E(ANGL)=22.299 | | E(DIHE)=0.000 E(IMPR)=9.439 E(VDW )=13.206 E(ELEC)=5.281 | | E(CDIH)=5.378 E(NOE )=18.462 E(PLAN)=2.151 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=1789.751 E(kin)=605.461 temperature=300.031 | | Etotal =1184.290 grad(E)=57.100 E(BOND)=225.371 E(ANGL)=577.292 | | E(DIHE)=0.000 E(IMPR)=125.912 E(VDW )=-40.980 E(ELEC)=-125.785 | | E(CDIH)=26.300 E(NOE )=377.741 E(PLAN)=18.438 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=135.074 E(kin)=14.436 temperature=7.154 | | Etotal =135.698 grad(E)=3.432 E(BOND)=33.326 E(ANGL)=90.479 | | E(DIHE)=0.000 E(IMPR)=12.972 E(VDW )=36.004 E(ELEC)=6.004 | | E(CDIH)=10.556 E(NOE )=33.413 E(PLAN)=3.701 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64820 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64859 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -12 -URI -H2' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64891 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64860 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64877 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64875 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64878 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64930 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64958 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65009 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65029 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=1720.323 E(kin)=608.109 temperature=301.344 | | Etotal =1112.214 grad(E)=60.027 E(BOND)=238.268 E(ANGL)=531.725 | | E(DIHE)=0.000 E(IMPR)=126.843 E(VDW )=-61.610 E(ELEC)=-129.730 | | E(CDIH)=17.033 E(NOE )=371.865 E(PLAN)=17.820 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65064 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65043 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 65015 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64927 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64865 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.50 A apart NBONDS: found 64863 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64888 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64910 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=1727.339 E(kin)=598.076 temperature=296.372 | | Etotal =1129.262 grad(E)=60.690 E(BOND)=223.776 E(ANGL)=551.748 | | E(DIHE)=0.000 E(IMPR)=105.569 E(VDW )=-68.664 E(ELEC)=-134.056 | | E(CDIH)=24.204 E(NOE )=411.130 E(PLAN)=15.557 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 64968 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64922 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64941 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65098 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65149 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65241 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65366 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65471 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65534 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65572 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=1722.714 E(kin)=607.947 temperature=301.263 | | Etotal =1114.767 grad(E)=58.552 E(BOND)=219.171 E(ANGL)=554.227 | | E(DIHE)=0.000 E(IMPR)=123.209 E(VDW )=-60.753 E(ELEC)=-128.052 | | E(CDIH)=28.910 E(NOE )=363.264 E(PLAN)=14.791 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65661 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65715 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65750 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65840 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65881 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 65847 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65890 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65943 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65949 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65925 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=1737.309 E(kin)=632.188 temperature=313.276 | | Etotal =1105.121 grad(E)=57.645 E(BOND)=207.364 E(ANGL)=559.175 | | E(DIHE)=0.000 E(IMPR)=118.408 E(VDW )=-63.115 E(ELEC)=-127.167 | | E(CDIH)=21.826 E(NOE )=368.077 E(PLAN)=20.553 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65853 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65854 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65950 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 65975 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 66029 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66055 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66118 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66157 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=1776.046 E(kin)=610.878 temperature=302.716 | | Etotal =1165.169 grad(E)=61.892 E(BOND)=256.277 E(ANGL)=573.832 | | E(DIHE)=0.000 E(IMPR)=132.811 E(VDW )=-63.892 E(ELEC)=-139.478 | | E(CDIH)=14.634 E(NOE )=368.922 E(PLAN)=22.061 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66192 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66199 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66188 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 66168 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 66164 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66113 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.48 A apart NBONDS: found 66134 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=1781.381 E(kin)=593.126 temperature=293.919 | | Etotal =1188.254 grad(E)=60.520 E(BOND)=255.359 E(ANGL)=575.979 | | E(DIHE)=0.000 E(IMPR)=121.578 E(VDW )=-72.741 E(ELEC)=-127.289 | | E(CDIH)=27.012 E(NOE )=387.534 E(PLAN)=20.823 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart NBONDS: found 66176 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66315 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66416 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66431 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66462 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66438 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 66410 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66389 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66335 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=1746.357 E(kin)=618.983 temperature=306.732 | | Etotal =1127.374 grad(E)=60.197 E(BOND)=221.457 E(ANGL)=573.872 | | E(DIHE)=0.000 E(IMPR)=119.319 E(VDW )=-79.990 E(ELEC)=-134.263 | | E(CDIH)=14.714 E(NOE )=397.302 E(PLAN)=14.963 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66250 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66259 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66192 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66075 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65963 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65862 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65783 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65676 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65660 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=1750.266 E(kin)=608.363 temperature=301.470 | | Etotal =1141.903 grad(E)=59.409 E(BOND)=232.918 E(ANGL)=572.535 | | E(DIHE)=0.000 E(IMPR)=138.334 E(VDW )=-69.897 E(ELEC)=-128.923 | | E(CDIH)=19.646 E(NOE )=362.593 E(PLAN)=14.696 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 65635 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65556 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65544 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65488 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65464 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65398 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65332 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65313 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65249 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=1752.172 E(kin)=614.458 temperature=304.490 | | Etotal =1137.715 grad(E)=60.003 E(BOND)=229.309 E(ANGL)=509.363 | | E(DIHE)=0.000 E(IMPR)=136.842 E(VDW )=-56.843 E(ELEC)=-124.532 | | E(CDIH)=35.080 E(NOE )=387.054 E(PLAN)=21.441 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65139 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65062 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65038 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 65001 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65001 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65050 intra-atom interactions NBONDS: found 65001 intra-atom interactions NBONDS: found 64936 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64867 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=1739.322 E(kin)=603.341 temperature=298.981 | | Etotal =1135.981 grad(E)=60.664 E(BOND)=256.158 E(ANGL)=546.321 | | E(DIHE)=0.000 E(IMPR)=112.009 E(VDW )=-42.430 E(ELEC)=-135.561 | | E(CDIH)=26.734 E(NOE )=353.663 E(PLAN)=19.086 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1742.529 E(kin)=605.410 temperature=300.006 | | Etotal =1137.119 grad(E)=60.457 E(BOND)=235.814 E(ANGL)=551.164 | | E(DIHE)=0.000 E(IMPR)=127.282 E(VDW )=-61.245 E(ELEC)=-130.265 | | E(CDIH)=23.059 E(NOE )=373.686 E(PLAN)=17.623 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=21.137 E(kin)=10.991 temperature=5.446 | | Etotal =23.526 grad(E)=1.321 E(BOND)=12.331 E(ANGL)=19.836 | | E(DIHE)=0.000 E(IMPR)=9.491 E(VDW )=13.962 E(ELEC)=4.533 | | E(CDIH)=5.312 E(NOE )=18.303 E(PLAN)=3.312 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=1780.306 E(kin)=605.451 temperature=300.026 | | Etotal =1174.856 grad(E)=57.772 E(BOND)=227.460 E(ANGL)=572.067 | | E(DIHE)=0.000 E(IMPR)=126.186 E(VDW )=-45.033 E(ELEC)=-126.681 | | E(CDIH)=25.652 E(NOE )=376.930 E(PLAN)=18.275 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=122.646 E(kin)=13.816 temperature=6.846 | | Etotal =123.279 grad(E)=3.402 E(BOND)=30.600 E(ANGL)=82.080 | | E(DIHE)=0.000 E(IMPR)=12.366 E(VDW )=33.789 E(ELEC)=6.013 | | E(CDIH)=9.822 E(NOE )=31.029 E(PLAN)=3.641 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64797 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64732 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64587 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64516 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64405 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64340 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64254 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64176 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64137 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64032 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=1736.347 E(kin)=595.308 temperature=295.000 | | Etotal =1141.039 grad(E)=61.977 E(BOND)=239.192 E(ANGL)=548.110 | | E(DIHE)=0.000 E(IMPR)=114.695 E(VDW )=-54.123 E(ELEC)=-126.726 | | E(CDIH)=10.004 E(NOE )=390.965 E(PLAN)=18.922 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64013 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 63995 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64087 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 64126 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64202 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64215 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64353 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64481 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64440 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64494 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=1737.504 E(kin)=601.368 temperature=298.003 | | Etotal =1136.136 grad(E)=59.915 E(BOND)=229.495 E(ANGL)=552.266 | | E(DIHE)=0.000 E(IMPR)=136.802 E(VDW )=-61.253 E(ELEC)=-129.731 | | E(CDIH)=18.821 E(NOE )=369.697 E(PLAN)=20.038 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64518 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64497 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.42 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64489 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64446 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64449 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64408 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64386 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64311 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64326 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64342 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64363 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64361 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64379 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=1743.548 E(kin)=608.972 temperature=301.771 | | Etotal =1134.576 grad(E)=62.385 E(BOND)=242.349 E(ANGL)=571.329 | | E(DIHE)=0.000 E(IMPR)=126.118 E(VDW )=-78.550 E(ELEC)=-128.928 | | E(CDIH)=22.688 E(NOE )=359.246 E(PLAN)=20.325 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64365 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64361 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64365 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64316 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64333 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64295 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64247 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64231 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64215 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64220 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64222 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=1740.177 E(kin)=585.634 temperature=290.206 | | Etotal =1154.543 grad(E)=61.832 E(BOND)=245.399 E(ANGL)=583.834 | | E(DIHE)=0.000 E(IMPR)=131.951 E(VDW )=-65.888 E(ELEC)=-124.552 | | E(CDIH)=11.846 E(NOE )=351.507 E(PLAN)=20.447 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64255 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64264 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64158 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64145 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64053 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63977 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.31 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63951 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63887 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=1768.200 E(kin)=607.656 temperature=301.119 | | Etotal =1160.545 grad(E)=62.279 E(BOND)=248.591 E(ANGL)=556.421 | | E(DIHE)=0.000 E(IMPR)=118.929 E(VDW )=-75.488 E(ELEC)=-128.875 | | E(CDIH)=23.550 E(NOE )=393.618 E(PLAN)=23.799 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63909 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63861 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63906 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63944 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63971 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64079 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64065 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=1801.151 E(kin)=629.701 temperature=312.043 | | Etotal =1171.450 grad(E)=62.396 E(BOND)=239.272 E(ANGL)=555.433 | | E(DIHE)=0.000 E(IMPR)=119.668 E(VDW )=-38.949 E(ELEC)=-126.340 | | E(CDIH)=26.996 E(NOE )=369.217 E(PLAN)=26.154 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64106 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64122 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64144 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64200 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 64309 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64300 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64357 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=1779.575 E(kin)=600.958 temperature=297.800 | | Etotal =1178.618 grad(E)=62.335 E(BOND)=256.472 E(ANGL)=564.661 | | E(DIHE)=0.000 E(IMPR)=138.814 E(VDW )=-75.879 E(ELEC)=-133.977 | | E(CDIH)=18.702 E(NOE )=390.579 E(PLAN)=19.245 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64443 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64514 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64591 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64750 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 64893 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64977 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 65026 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 65034 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=1754.908 E(kin)=594.912 temperature=294.804 | | Etotal =1159.996 grad(E)=63.424 E(BOND)=251.556 E(ANGL)=562.387 | | E(DIHE)=0.000 E(IMPR)=119.373 E(VDW )=-59.540 E(ELEC)=-128.127 | | E(CDIH)=22.067 E(NOE )=372.818 E(PLAN)=19.461 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 65012 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64988 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64970 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 65022 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 65044 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64999 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 65001 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64959 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64970 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64976 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64990 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65024 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=1708.154 E(kin)=601.203 temperature=297.921 | | Etotal =1106.951 grad(E)=61.678 E(BOND)=245.400 E(ANGL)=541.705 | | E(DIHE)=0.000 E(IMPR)=114.764 E(VDW )=-53.758 E(ELEC)=-135.815 | | E(CDIH)=29.187 E(NOE )=348.009 E(PLAN)=17.458 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65058 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 65077 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65135 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65114 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65124 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 65125 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65089 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65035 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65077 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64993 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64928 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=1725.873 E(kin)=604.924 temperature=299.765 | | Etotal =1120.948 grad(E)=61.629 E(BOND)=243.853 E(ANGL)=538.307 | | E(DIHE)=0.000 E(IMPR)=123.936 E(VDW )=-49.149 E(ELEC)=-139.230 | | E(CDIH)=18.249 E(NOE )=365.665 E(PLAN)=19.318 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1751.486 E(kin)=605.524 temperature=300.063 | | Etotal =1145.962 grad(E)=61.560 E(BOND)=242.963 E(ANGL)=555.788 | | E(DIHE)=0.000 E(IMPR)=125.159 E(VDW )=-62.762 E(ELEC)=-130.031 | | E(CDIH)=22.049 E(NOE )=372.925 E(PLAN)=19.871 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=22.806 E(kin)=11.732 temperature=5.814 | | Etotal =25.441 grad(E)=1.306 E(BOND)=11.951 E(ANGL)=20.242 | | E(DIHE)=0.000 E(IMPR)=9.299 E(VDW )=12.898 E(ELEC)=4.964 | | E(CDIH)=4.774 E(NOE )=16.561 E(PLAN)=2.706 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=1775.503 E(kin)=605.463 temperature=300.032 | | Etotal =1170.040 grad(E)=58.403 E(BOND)=230.044 E(ANGL)=569.354 | | E(DIHE)=0.000 E(IMPR)=126.015 E(VDW )=-47.988 E(ELEC)=-127.239 | | E(CDIH)=25.051 E(NOE )=376.262 E(PLAN)=18.541 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=112.859 E(kin)=13.491 temperature=6.685 | | Etotal =113.528 grad(E)=3.453 E(BOND)=28.939 E(ANGL)=75.626 | | E(DIHE)=0.000 E(IMPR)=11.916 E(VDW )=31.981 E(ELEC)=5.983 | | E(CDIH)=9.273 E(NOE )=29.159 E(PLAN)=3.553 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.49 A apart NBONDS: found 64934 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64923 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64896 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 64860 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64831 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64745 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64732 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64759 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64760 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64802 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=1736.148 E(kin)=591.283 temperature=293.006 | | Etotal =1144.864 grad(E)=63.964 E(BOND)=255.243 E(ANGL)=556.411 | | E(DIHE)=0.000 E(IMPR)=135.006 E(VDW )=-66.959 E(ELEC)=-129.172 | | E(CDIH)=27.706 E(NOE )=346.184 E(PLAN)=20.445 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64908 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64967 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65042 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65118 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65190 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65241 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65312 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65377 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65421 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65487 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=1735.603 E(kin)=612.017 temperature=303.280 | | Etotal =1123.587 grad(E)=61.112 E(BOND)=242.790 E(ANGL)=544.232 | | E(DIHE)=0.000 E(IMPR)=124.191 E(VDW )=-56.153 E(ELEC)=-134.997 | | E(CDIH)=21.457 E(NOE )=365.326 E(PLAN)=16.741 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 65537 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65621 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65692 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65738 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65707 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65749 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65827 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65896 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=1722.481 E(kin)=613.632 temperature=304.080 | | Etotal =1108.849 grad(E)=60.546 E(BOND)=243.209 E(ANGL)=542.713 | | E(DIHE)=0.000 E(IMPR)=123.132 E(VDW )=-50.251 E(ELEC)=-143.811 | | E(CDIH)=20.959 E(NOE )=353.118 E(PLAN)=19.780 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 66018 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 66087 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66122 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66179 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66237 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66268 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66291 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66303 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 66380 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 66435 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=1756.043 E(kin)=594.700 temperature=294.699 | | Etotal =1161.342 grad(E)=63.495 E(BOND)=228.406 E(ANGL)=578.121 | | E(DIHE)=0.000 E(IMPR)=140.256 E(VDW )=-62.949 E(ELEC)=-141.921 | | E(CDIH)=18.500 E(NOE )=387.061 E(PLAN)=13.869 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 66386 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66423 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 66360 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66294 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66242 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66224 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66242 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66252 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66226 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66168 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=1771.033 E(kin)=605.236 temperature=299.920 | | Etotal =1165.797 grad(E)=64.594 E(BOND)=270.001 E(ANGL)=550.399 | | E(DIHE)=0.000 E(IMPR)=119.922 E(VDW )=-56.550 E(ELEC)=-141.521 | | E(CDIH)=30.600 E(NOE )=377.251 E(PLAN)=15.696 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 66122 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart NBONDS: found 66148 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66149 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 66184 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66240 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.36 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66292 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66323 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.49 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66366 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66385 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66403 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66427 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66477 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=1766.547 E(kin)=626.095 temperature=310.256 | | Etotal =1140.453 grad(E)=61.067 E(BOND)=237.107 E(ANGL)=563.052 | | E(DIHE)=0.000 E(IMPR)=109.120 E(VDW )=-45.445 E(ELEC)=-140.684 | | E(CDIH)=21.060 E(NOE )=381.798 E(PLAN)=14.445 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66452 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66453 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66422 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66470 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 66422 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66363 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 66425 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 66412 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.35 A apart NBONDS: found 66431 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66401 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 66346 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=1779.936 E(kin)=613.601 temperature=304.065 | | Etotal =1166.335 grad(E)=63.798 E(BOND)=237.223 E(ANGL)=560.224 | | E(DIHE)=0.000 E(IMPR)=127.699 E(VDW )=-42.745 E(ELEC)=-139.343 | | E(CDIH)=25.552 E(NOE )=380.280 E(PLAN)=17.444 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66307 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66280 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66285 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66307 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66315 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66400 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66458 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66434 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66445 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=1770.309 E(kin)=621.047 temperature=307.755 | | Etotal =1149.263 grad(E)=64.429 E(BOND)=246.218 E(ANGL)=502.889 | | E(DIHE)=0.000 E(IMPR)=133.324 E(VDW )=-40.045 E(ELEC)=-129.825 | | E(CDIH)=37.711 E(NOE )=380.517 E(PLAN)=18.474 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66429 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66346 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66321 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66285 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66207 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66198 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66195 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66237 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=1745.078 E(kin)=604.910 temperature=299.758 | | Etotal =1140.168 grad(E)=64.125 E(BOND)=252.614 E(ANGL)=540.331 | | E(DIHE)=0.000 E(IMPR)=139.651 E(VDW )=-85.734 E(ELEC)=-133.272 | | E(CDIH)=17.927 E(NOE )=393.943 E(PLAN)=14.709 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66277 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66271 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66274 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66238 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.38 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 66107 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.31 A apart NBONDS: found 66006 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65882 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=1729.421 E(kin)=622.077 temperature=308.265 | | Etotal =1107.344 grad(E)=63.047 E(BOND)=245.151 E(ANGL)=535.081 | | E(DIHE)=0.000 E(IMPR)=130.849 E(VDW )=-60.593 E(ELEC)=-137.248 | | E(CDIH)=25.003 E(NOE )=355.365 E(PLAN)=13.735 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1749.375 E(kin)=605.454 temperature=300.028 | | Etotal =1143.921 grad(E)=63.361 E(BOND)=246.079 E(ANGL)=550.750 | | E(DIHE)=0.000 E(IMPR)=128.161 E(VDW )=-58.036 E(ELEC)=-136.630 | | E(CDIH)=23.409 E(NOE )=374.312 E(PLAN)=15.876 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=20.524 E(kin)=11.720 temperature=5.808 | | Etotal =23.314 grad(E)=1.644 E(BOND)=10.940 E(ANGL)=17.110 | | E(DIHE)=0.000 E(IMPR)=10.204 E(VDW )=13.490 E(ELEC)=5.888 | | E(CDIH)=4.941 E(NOE )=16.492 E(PLAN)=2.434 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=1771.770 E(kin)=605.462 temperature=300.032 | | Etotal =1166.309 grad(E)=59.111 E(BOND)=232.334 E(ANGL)=566.696 | | E(DIHE)=0.000 E(IMPR)=126.322 E(VDW )=-49.423 E(ELEC)=-128.581 | | E(CDIH)=24.817 E(NOE )=375.984 E(PLAN)=18.160 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=105.173 E(kin)=13.252 temperature=6.567 | | Etotal =105.871 grad(E)=3.690 E(BOND)=27.684 E(ANGL)=70.615 | | E(DIHE)=0.000 E(IMPR)=11.711 E(VDW )=30.250 E(ELEC)=6.814 | | E(CDIH)=8.805 E(NOE )=27.715 E(PLAN)=3.540 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65774 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65664 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65580 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65588 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65516 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65492 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65431 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65399 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65387 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=1744.050 E(kin)=610.814 temperature=302.684 | | Etotal =1133.236 grad(E)=62.186 E(BOND)=262.558 E(ANGL)=530.409 | | E(DIHE)=0.000 E(IMPR)=115.040 E(VDW )=-59.954 E(ELEC)=-141.193 | | E(CDIH)=19.543 E(NOE )=392.375 E(PLAN)=14.458 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65381 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65358 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65282 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65241 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65220 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65252 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=1749.453 E(kin)=605.845 temperature=300.221 | | Etotal =1143.608 grad(E)=65.393 E(BOND)=242.893 E(ANGL)=581.161 | | E(DIHE)=0.000 E(IMPR)=127.655 E(VDW )=-50.773 E(ELEC)=-138.536 | | E(CDIH)=14.727 E(NOE )=348.878 E(PLAN)=17.603 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65163 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65122 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65041 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -11 -ADE -H61 " and "A -13 -ADE -H5''" only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64969 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64924 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=1750.305 E(kin)=623.616 temperature=309.028 | | Etotal =1126.690 grad(E)=63.718 E(BOND)=220.749 E(ANGL)=550.619 | | E(DIHE)=0.000 E(IMPR)=134.637 E(VDW )=-49.345 E(ELEC)=-121.568 | | E(CDIH)=26.974 E(NOE )=350.620 E(PLAN)=14.004 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64923 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64898 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64929 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64981 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65099 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 65187 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=1734.870 E(kin)=626.926 temperature=310.668 | | Etotal =1107.944 grad(E)=61.620 E(BOND)=225.875 E(ANGL)=541.124 | | E(DIHE)=0.000 E(IMPR)=124.662 E(VDW )=-44.802 E(ELEC)=-143.413 | | E(CDIH)=17.510 E(NOE )=365.302 E(PLAN)=21.686 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65276 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65304 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65279 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65264 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65272 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65204 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65169 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65138 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65080 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=1752.306 E(kin)=603.452 temperature=299.036 | | Etotal =1148.854 grad(E)=64.859 E(BOND)=254.871 E(ANGL)=560.861 | | E(DIHE)=0.000 E(IMPR)=140.743 E(VDW )=-74.723 E(ELEC)=-138.274 | | E(CDIH)=24.690 E(NOE )=361.922 E(PLAN)=18.764 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65028 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64994 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64882 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 64737 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart NBONDS: found 64715 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64738 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64729 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64752 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=1744.633 E(kin)=634.566 temperature=314.454 | | Etotal =1110.067 grad(E)=63.718 E(BOND)=240.821 E(ANGL)=536.717 | | E(DIHE)=0.000 E(IMPR)=122.931 E(VDW )=-61.804 E(ELEC)=-141.272 | | E(CDIH)=23.208 E(NOE )=375.484 E(PLAN)=13.981 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64761 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64757 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64724 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -9 -URI -H5' " only 1.48 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64707 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64595 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64455 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 64332 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64254 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=1757.298 E(kin)=604.912 temperature=299.760 | | Etotal =1152.386 grad(E)=64.724 E(BOND)=243.599 E(ANGL)=556.680 | | E(DIHE)=0.000 E(IMPR)=136.563 E(VDW )=-71.153 E(ELEC)=-129.453 | | E(CDIH)=29.160 E(NOE )=369.734 E(PLAN)=17.255 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64194 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64119 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64130 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64048 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 64075 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 64049 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 64071 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64055 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64037 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=1746.836 E(kin)=591.361 temperature=293.044 | | Etotal =1155.474 grad(E)=66.075 E(BOND)=244.548 E(ANGL)=573.843 | | E(DIHE)=0.000 E(IMPR)=125.931 E(VDW )=-72.383 E(ELEC)=-134.174 | | E(CDIH)=34.302 E(NOE )=364.099 E(PLAN)=19.308 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64018 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63991 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63979 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63954 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63971 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63929 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63938 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 63859 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63832 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 63732 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63706 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=1766.899 E(kin)=608.821 temperature=301.696 | | Etotal =1158.078 grad(E)=64.756 E(BOND)=246.468 E(ANGL)=555.456 | | E(DIHE)=0.000 E(IMPR)=134.128 E(VDW )=-50.521 E(ELEC)=-128.279 | | E(CDIH)=21.118 E(NOE )=356.604 E(PLAN)=23.104 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63548 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 63408 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63353 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 63353 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63392 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=1764.174 E(kin)=578.865 temperature=286.852 | | Etotal =1185.309 grad(E)=63.369 E(BOND)=243.249 E(ANGL)=609.630 | | E(DIHE)=0.000 E(IMPR)=119.680 E(VDW )=-82.038 E(ELEC)=-131.402 | | E(CDIH)=21.604 E(NOE )=381.039 E(PLAN)=23.547 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1749.887 E(kin)=605.310 temperature=299.956 | | Etotal =1144.577 grad(E)=64.147 E(BOND)=244.901 E(ANGL)=554.724 | | E(DIHE)=0.000 E(IMPR)=130.873 E(VDW )=-61.921 E(ELEC)=-134.525 | | E(CDIH)=22.623 E(NOE )=369.264 E(PLAN)=18.639 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.485 E(kin)=11.779 temperature=5.837 | | Etotal =16.714 grad(E)=1.363 E(BOND)=12.265 E(ANGL)=19.520 | | E(DIHE)=0.000 E(IMPR)=10.188 E(VDW )=13.061 E(ELEC)=5.528 | | E(CDIH)=4.870 E(NOE )=14.704 E(PLAN)=2.993 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=1769.035 E(kin)=605.443 temperature=300.022 | | Etotal =1163.592 grad(E)=59.741 E(BOND)=233.905 E(ANGL)=565.200 | | E(DIHE)=0.000 E(IMPR)=126.891 E(VDW )=-50.985 E(ELEC)=-129.324 | | E(CDIH)=24.543 E(NOE )=375.144 E(PLAN)=18.220 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=98.745 E(kin)=13.077 temperature=6.480 | | Etotal =99.469 grad(E)=3.863 E(BOND)=26.583 E(ANGL)=66.532 | | E(DIHE)=0.000 E(IMPR)=11.630 E(VDW )=28.967 E(ELEC)=6.951 | | E(CDIH)=8.445 E(NOE )=26.534 E(PLAN)=3.480 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63470 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63567 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 63629 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63729 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63834 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63861 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63920 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=1736.195 E(kin)=596.839 temperature=295.759 | | Etotal =1139.356 grad(E)=64.392 E(BOND)=245.172 E(ANGL)=552.365 | | E(DIHE)=0.000 E(IMPR)=111.839 E(VDW )=-38.827 E(ELEC)=-136.912 | | E(CDIH)=19.757 E(NOE )=369.916 E(PLAN)=16.047 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63942 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64010 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64015 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64015 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64065 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64102 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64118 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64176 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=1729.273 E(kin)=596.682 temperature=295.681 | | Etotal =1132.591 grad(E)=62.351 E(BOND)=225.612 E(ANGL)=572.262 | | E(DIHE)=0.000 E(IMPR)=129.157 E(VDW )=-66.594 E(ELEC)=-128.301 | | E(CDIH)=19.786 E(NOE )=364.552 E(PLAN)=16.116 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64243 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64350 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 64518 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64625 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64696 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64734 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64750 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=1745.001 E(kin)=598.353 temperature=296.509 | | Etotal =1146.648 grad(E)=62.990 E(BOND)=246.084 E(ANGL)=565.452 | | E(DIHE)=0.000 E(IMPR)=118.416 E(VDW )=-39.018 E(ELEC)=-141.490 | | E(CDIH)=16.882 E(NOE )=357.340 E(PLAN)=22.982 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 64814 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64952 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65041 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65083 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65072 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65098 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65203 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=1756.199 E(kin)=601.456 temperature=298.047 | | Etotal =1154.743 grad(E)=64.088 E(BOND)=239.051 E(ANGL)=569.510 | | E(DIHE)=0.000 E(IMPR)=131.769 E(VDW )=-51.503 E(ELEC)=-131.580 | | E(CDIH)=15.379 E(NOE )=361.949 E(PLAN)=20.168 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65291 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65370 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65479 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65561 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65722 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65757 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 65846 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65985 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=1744.887 E(kin)=593.757 temperature=294.232 | | Etotal =1151.130 grad(E)=63.015 E(BOND)=261.727 E(ANGL)=557.621 | | E(DIHE)=0.000 E(IMPR)=130.892 E(VDW )=-99.179 E(ELEC)=-129.691 | | E(CDIH)=19.567 E(NOE )=395.296 E(PLAN)=14.896 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66089 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 66220 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66294 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66342 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66400 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66385 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 66426 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.35 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 66402 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 66288 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=1754.013 E(kin)=606.278 temperature=300.436 | | Etotal =1147.735 grad(E)=61.861 E(BOND)=240.364 E(ANGL)=546.655 | | E(DIHE)=0.000 E(IMPR)=134.859 E(VDW )=-52.892 E(ELEC)=-139.906 | | E(CDIH)=18.592 E(NOE )=381.681 E(PLAN)=18.383 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66223 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 66156 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66077 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66009 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65987 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65890 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65903 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65898 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65917 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=1755.486 E(kin)=598.678 temperature=296.670 | | Etotal =1156.808 grad(E)=63.861 E(BOND)=262.847 E(ANGL)=563.725 | | E(DIHE)=0.000 E(IMPR)=121.485 E(VDW )=-48.324 E(ELEC)=-139.100 | | E(CDIH)=27.579 E(NOE )=353.595 E(PLAN)=14.999 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65899 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65842 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65803 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65769 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65717 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65626 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65550 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 65495 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65417 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65269 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=1776.762 E(kin)=611.061 temperature=302.807 | | Etotal =1165.701 grad(E)=64.908 E(BOND)=268.806 E(ANGL)=566.913 | | E(DIHE)=0.000 E(IMPR)=110.633 E(VDW )=-67.384 E(ELEC)=-135.462 | | E(CDIH)=24.184 E(NOE )=378.404 E(PLAN)=19.607 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65087 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64948 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64847 intra-atom interactions NBONDS: found 64709 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64698 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64696 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64761 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64804 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=1761.950 E(kin)=609.169 temperature=301.869 | | Etotal =1152.781 grad(E)=65.308 E(BOND)=240.185 E(ANGL)=560.914 | | E(DIHE)=0.000 E(IMPR)=118.167 E(VDW )=-49.152 E(ELEC)=-132.389 | | E(CDIH)=24.218 E(NOE )=371.077 E(PLAN)=19.761 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64804 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64815 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64886 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64957 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65094 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 65221 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65278 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65335 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65360 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65393 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=1732.431 E(kin)=611.727 temperature=303.136 | | Etotal =1120.703 grad(E)=64.059 E(BOND)=241.400 E(ANGL)=558.557 | | E(DIHE)=0.000 E(IMPR)=133.456 E(VDW )=-64.265 E(ELEC)=-130.049 | | E(CDIH)=26.185 E(NOE )=338.733 E(PLAN)=16.685 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1755.640 E(kin)=605.602 temperature=300.101 | | Etotal =1150.038 grad(E)=63.987 E(BOND)=250.760 E(ANGL)=559.417 | | E(DIHE)=0.000 E(IMPR)=127.612 E(VDW )=-62.509 E(ELEC)=-132.319 | | E(CDIH)=22.077 E(NOE )=367.309 E(PLAN)=17.691 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=18.269 E(kin)=12.463 temperature=6.176 | | Etotal =21.795 grad(E)=1.385 E(BOND)=12.272 E(ANGL)=17.620 | | E(DIHE)=0.000 E(IMPR)=8.966 E(VDW )=11.861 E(ELEC)=5.422 | | E(CDIH)=4.776 E(NOE )=13.881 E(PLAN)=2.454 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=1767.547 E(kin)=605.460 temperature=300.031 | | Etotal =1162.086 grad(E)=60.213 E(BOND)=235.778 E(ANGL)=564.557 | | E(DIHE)=0.000 E(IMPR)=126.971 E(VDW )=-52.266 E(ELEC)=-129.656 | | E(CDIH)=24.269 E(NOE )=374.273 E(PLAN)=18.161 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=93.391 E(kin)=13.011 temperature=6.447 | | Etotal =94.158 grad(E)=3.906 E(BOND)=25.941 E(ANGL)=63.027 | | E(DIHE)=0.000 E(IMPR)=11.367 E(VDW )=27.831 E(ELEC)=6.863 | | E(CDIH)=8.157 E(NOE )=25.560 E(PLAN)=3.386 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65410 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65525 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65614 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65651 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 65655 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 65644 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65640 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65576 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=1747.097 E(kin)=599.169 temperature=296.913 | | Etotal =1147.928 grad(E)=64.165 E(BOND)=254.960 E(ANGL)=577.575 | | E(DIHE)=0.000 E(IMPR)=139.153 E(VDW )=-44.370 E(ELEC)=-131.561 | | E(CDIH)=16.713 E(NOE )=319.577 E(PLAN)=15.880 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65419 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65344 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65258 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65239 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65262 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65329 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65312 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65403 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=1738.979 E(kin)=610.472 temperature=302.515 | | Etotal =1128.507 grad(E)=64.046 E(BOND)=253.335 E(ANGL)=565.377 | | E(DIHE)=0.000 E(IMPR)=112.530 E(VDW )=-76.610 E(ELEC)=-137.955 | | E(CDIH)=27.280 E(NOE )=367.078 E(PLAN)=17.474 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65456 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65530 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65566 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 65566 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 65535 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65441 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 65296 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 65107 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=1746.878 E(kin)=607.836 temperature=301.208 | | Etotal =1139.043 grad(E)=65.474 E(BOND)=263.770 E(ANGL)=532.210 | | E(DIHE)=0.000 E(IMPR)=137.255 E(VDW )=-60.396 E(ELEC)=-128.833 | | E(CDIH)=20.485 E(NOE )=356.267 E(PLAN)=18.283 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65064 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64947 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64893 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64919 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 64826 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64838 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64817 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64894 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=1733.595 E(kin)=608.353 temperature=301.465 | | Etotal =1125.241 grad(E)=64.094 E(BOND)=257.008 E(ANGL)=545.032 | | E(DIHE)=0.000 E(IMPR)=125.054 E(VDW )=-71.096 E(ELEC)=-134.247 | | E(CDIH)=25.606 E(NOE )=361.192 E(PLAN)=16.692 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64868 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64889 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64967 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65023 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 65103 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65137 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 65186 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=1748.324 E(kin)=598.470 temperature=296.567 | | Etotal =1149.854 grad(E)=65.564 E(BOND)=248.335 E(ANGL)=578.003 | | E(DIHE)=0.000 E(IMPR)=132.128 E(VDW )=-47.536 E(ELEC)=-143.462 | | E(CDIH)=22.965 E(NOE )=344.020 E(PLAN)=15.402 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65181 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65111 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65078 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64924 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64801 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 64786 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64640 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=1741.087 E(kin)=577.728 temperature=286.288 | | Etotal =1163.359 grad(E)=65.832 E(BOND)=252.818 E(ANGL)=566.345 | | E(DIHE)=0.000 E(IMPR)=123.835 E(VDW )=-30.089 E(ELEC)=-137.438 | | E(CDIH)=25.185 E(NOE )=348.609 E(PLAN)=14.095 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64540 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64437 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64356 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64314 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 64351 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64409 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=1748.220 E(kin)=617.168 temperature=305.833 | | Etotal =1131.052 grad(E)=66.155 E(BOND)=243.143 E(ANGL)=558.540 | | E(DIHE)=0.000 E(IMPR)=132.898 E(VDW )=-72.138 E(ELEC)=-146.352 | | E(CDIH)=18.929 E(NOE )=375.352 E(PLAN)=20.680 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64447 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64474 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64534 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64502 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64554 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64568 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 64505 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64502 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=1772.077 E(kin)=605.549 temperature=300.075 | | Etotal =1166.528 grad(E)=65.131 E(BOND)=252.689 E(ANGL)=554.100 | | E(DIHE)=0.000 E(IMPR)=134.560 E(VDW )=-81.416 E(ELEC)=-150.438 | | E(CDIH)=19.581 E(NOE )=411.513 E(PLAN)=25.940 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64461 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64344 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64290 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.46 A apart NBONDS: found 64356 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64351 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64431 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64462 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64518 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=1783.356 E(kin)=589.509 temperature=292.126 | | Etotal =1193.847 grad(E)=68.110 E(BOND)=289.058 E(ANGL)=558.285 | | E(DIHE)=0.000 E(IMPR)=142.957 E(VDW )=-60.716 E(ELEC)=-139.540 | | E(CDIH)=21.613 E(NOE )=361.103 E(PLAN)=21.086 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64548 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64534 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64508 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64432 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64372 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64329 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64343 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=1782.689 E(kin)=620.720 temperature=307.593 | | Etotal =1161.968 grad(E)=62.872 E(BOND)=234.149 E(ANGL)=551.996 | | E(DIHE)=0.000 E(IMPR)=134.852 E(VDW )=-47.840 E(ELEC)=-133.065 | | E(CDIH)=23.902 E(NOE )=382.819 E(PLAN)=15.156 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1751.436 E(kin)=605.268 temperature=299.936 | | Etotal =1146.168 grad(E)=64.924 E(BOND)=253.034 E(ANGL)=556.943 | | E(DIHE)=0.000 E(IMPR)=128.767 E(VDW )=-64.672 E(ELEC)=-138.252 | | E(CDIH)=22.847 E(NOE )=369.082 E(PLAN)=18.418 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=14.764 E(kin)=12.404 temperature=6.147 | | Etotal =18.913 grad(E)=1.586 E(BOND)=11.951 E(ANGL)=15.791 | | E(DIHE)=0.000 E(IMPR)=9.999 E(VDW )=11.592 E(ELEC)=5.795 | | E(CDIH)=4.673 E(NOE )=16.221 E(PLAN)=3.021 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=1765.935 E(kin)=605.441 temperature=300.022 | | Etotal =1160.494 grad(E)=60.684 E(BOND)=237.503 E(ANGL)=563.796 | | E(DIHE)=0.000 E(IMPR)=127.150 E(VDW )=-53.506 E(ELEC)=-130.516 | | E(CDIH)=24.126 E(NOE )=373.754 E(PLAN)=18.187 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=88.853 E(kin)=12.951 temperature=6.418 | | Etotal =89.653 grad(E)=3.998 E(BOND)=25.431 E(ANGL)=60.045 | | E(DIHE)=0.000 E(IMPR)=11.250 E(VDW )=26.915 E(ELEC)=7.239 | | E(CDIH)=7.890 E(NOE )=24.834 E(PLAN)=3.352 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.32 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64346 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64366 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64386 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -11 -ADE -H8 " and "A -12 -URI -O4' " only 1.50 A apart NBONDS: found 64465 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64523 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64631 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64692 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64733 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=1732.335 E(kin)=616.410 temperature=305.457 | | Etotal =1115.925 grad(E)=65.109 E(BOND)=234.484 E(ANGL)=524.889 | | E(DIHE)=0.000 E(IMPR)=128.719 E(VDW )=-25.914 E(ELEC)=-149.658 | | E(CDIH)=24.359 E(NOE )=358.841 E(PLAN)=20.204 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64763 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64776 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64799 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64773 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64766 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64751 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 64771 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64747 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64669 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64663 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=1750.441 E(kin)=598.636 temperature=296.649 | | Etotal =1151.804 grad(E)=66.057 E(BOND)=254.069 E(ANGL)=609.192 | | E(DIHE)=0.000 E(IMPR)=121.167 E(VDW )=-68.258 E(ELEC)=-144.865 | | E(CDIH)=22.961 E(NOE )=340.948 E(PLAN)=16.591 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 64692 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64737 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64778 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64803 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64799 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64809 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64842 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64909 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64896 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64928 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=1732.410 E(kin)=573.021 temperature=283.956 | | Etotal =1159.389 grad(E)=67.399 E(BOND)=256.267 E(ANGL)=556.474 | | E(DIHE)=0.000 E(IMPR)=131.338 E(VDW )=-57.860 E(ELEC)=-136.812 | | E(CDIH)=26.000 E(NOE )=367.528 E(PLAN)=16.455 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64941 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64951 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 64974 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 65023 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 65040 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65021 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65035 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65069 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65096 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65079 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=1746.354 E(kin)=600.524 temperature=297.585 | | Etotal =1145.830 grad(E)=67.080 E(BOND)=251.961 E(ANGL)=561.633 | | E(DIHE)=0.000 E(IMPR)=140.616 E(VDW )=-62.556 E(ELEC)=-149.339 | | E(CDIH)=17.285 E(NOE )=370.325 E(PLAN)=15.906 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65096 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65070 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65037 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64998 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64972 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 64863 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64862 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64863 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64846 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=1734.298 E(kin)=610.685 temperature=302.620 | | Etotal =1123.613 grad(E)=64.944 E(BOND)=230.636 E(ANGL)=565.074 | | E(DIHE)=0.000 E(IMPR)=127.638 E(VDW )=-79.717 E(ELEC)=-147.573 | | E(CDIH)=20.354 E(NOE )=388.157 E(PLAN)=19.044 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64844 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64905 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65007 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65024 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65090 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65124 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 65174 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 65181 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart NBONDS: found 65222 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=1751.125 E(kin)=603.442 temperature=299.031 | | Etotal =1147.682 grad(E)=67.105 E(BOND)=251.827 E(ANGL)=577.972 | | E(DIHE)=0.000 E(IMPR)=122.116 E(VDW )=-70.898 E(ELEC)=-140.550 | | E(CDIH)=21.631 E(NOE )=368.363 E(PLAN)=17.222 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65190 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 65191 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 65087 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart NBONDS: found 65059 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65050 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65004 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65016 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart NBONDS: found 65037 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=1750.818 E(kin)=605.079 temperature=299.842 | | Etotal =1145.739 grad(E)=66.890 E(BOND)=256.391 E(ANGL)=563.814 | | E(DIHE)=0.000 E(IMPR)=144.699 E(VDW )=-66.633 E(ELEC)=-136.932 | | E(CDIH)=18.125 E(NOE )=348.041 E(PLAN)=18.236 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65012 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65003 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 65030 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65063 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65054 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65048 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=1736.499 E(kin)=616.699 temperature=305.600 | | Etotal =1119.800 grad(E)=64.972 E(BOND)=244.437 E(ANGL)=548.083 | | E(DIHE)=0.000 E(IMPR)=119.203 E(VDW )=-62.966 E(ELEC)=-141.280 | | E(CDIH)=26.926 E(NOE )=371.797 E(PLAN)=13.599 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65063 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 65020 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65093 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65159 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65239 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 65334 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65374 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=1761.000 E(kin)=594.408 temperature=294.554 | | Etotal =1166.592 grad(E)=67.367 E(BOND)=257.838 E(ANGL)=569.310 | | E(DIHE)=0.000 E(IMPR)=134.170 E(VDW )=-69.224 E(ELEC)=-136.410 | | E(CDIH)=32.669 E(NOE )=359.989 E(PLAN)=18.250 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65423 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65489 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65530 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65601 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65613 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65628 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65623 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65584 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=1771.249 E(kin)=586.789 temperature=290.779 | | Etotal =1184.461 grad(E)=68.294 E(BOND)=263.824 E(ANGL)=585.739 | | E(DIHE)=0.000 E(IMPR)=141.487 E(VDW )=-62.673 E(ELEC)=-133.528 | | E(CDIH)=20.230 E(NOE )=353.642 E(PLAN)=15.739 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1749.525 E(kin)=605.515 temperature=300.058 | | Etotal =1144.010 grad(E)=66.394 E(BOND)=253.626 E(ANGL)=558.970 | | E(DIHE)=0.000 E(IMPR)=131.612 E(VDW )=-63.597 E(ELEC)=-141.325 | | E(CDIH)=22.820 E(NOE )=364.347 E(PLAN)=17.557 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.932 E(kin)=12.388 temperature=6.139 | | Etotal =17.494 grad(E)=1.400 E(BOND)=11.478 E(ANGL)=15.798 | | E(DIHE)=0.000 E(IMPR)=9.239 E(VDW )=11.602 E(ELEC)=5.558 | | E(CDIH)=4.538 E(NOE )=14.182 E(PLAN)=2.220 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=1764.444 E(kin)=605.448 temperature=300.025 | | Etotal =1158.996 grad(E)=61.203 E(BOND)=238.969 E(ANGL)=563.357 | | E(DIHE)=0.000 E(IMPR)=127.556 E(VDW )=-54.424 E(ELEC)=-131.499 | | E(CDIH)=24.008 E(NOE )=372.899 E(PLAN)=18.130 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=84.939 E(kin)=12.901 temperature=6.393 | | Etotal =85.775 grad(E)=4.171 E(BOND)=24.928 E(ANGL)=57.465 | | E(DIHE)=0.000 E(IMPR)=11.157 E(VDW )=26.062 E(ELEC)=7.752 | | E(CDIH)=7.655 E(NOE )=24.213 E(PLAN)=3.270 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 65506 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 65488 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65467 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65439 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65414 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 65435 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=1754.928 E(kin)=605.904 temperature=300.251 | | Etotal =1149.024 grad(E)=65.066 E(BOND)=251.452 E(ANGL)=568.916 | | E(DIHE)=0.000 E(IMPR)=117.869 E(VDW )=-62.240 E(ELEC)=-137.088 | | E(CDIH)=22.011 E(NOE )=371.910 E(PLAN)=16.195 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65465 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65497 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65472 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65515 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65462 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65422 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 65361 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=1762.843 E(kin)=624.343 temperature=309.388 | | Etotal =1138.500 grad(E)=64.460 E(BOND)=245.707 E(ANGL)=546.164 | | E(DIHE)=0.000 E(IMPR)=128.661 E(VDW )=-65.522 E(ELEC)=-128.783 | | E(CDIH)=25.177 E(NOE )=371.725 E(PLAN)=15.372 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart NBONDS: found 65277 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65120 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65088 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 65042 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65061 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65020 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=1759.153 E(kin)=610.319 temperature=302.439 | | Etotal =1148.834 grad(E)=67.492 E(BOND)=256.186 E(ANGL)=548.611 | | E(DIHE)=0.000 E(IMPR)=133.800 E(VDW )=-71.550 E(ELEC)=-132.765 | | E(CDIH)=23.179 E(NOE )=369.817 E(PLAN)=21.556 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65037 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65130 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 65105 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 65093 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65044 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 65103 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65053 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=1766.732 E(kin)=592.997 temperature=293.855 | | Etotal =1173.735 grad(E)=66.014 E(BOND)=257.123 E(ANGL)=556.254 | | E(DIHE)=0.000 E(IMPR)=142.762 E(VDW )=-64.504 E(ELEC)=-136.451 | | E(CDIH)=23.665 E(NOE )=377.022 E(PLAN)=17.863 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65033 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65047 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65037 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64960 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64820 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64711 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64666 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64639 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64627 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=1741.443 E(kin)=630.483 temperature=312.431 | | Etotal =1110.960 grad(E)=64.868 E(BOND)=233.611 E(ANGL)=525.934 | | E(DIHE)=0.000 E(IMPR)=138.954 E(VDW )=-59.924 E(ELEC)=-134.086 | | E(CDIH)=25.088 E(NOE )=365.168 E(PLAN)=16.216 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64599 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64582 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64580 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64560 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64491 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64509 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64491 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64509 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64513 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64512 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=1748.070 E(kin)=607.760 temperature=301.170 | | Etotal =1140.310 grad(E)=65.145 E(BOND)=237.944 E(ANGL)=584.539 | | E(DIHE)=0.000 E(IMPR)=116.417 E(VDW )=-65.005 E(ELEC)=-141.764 | | E(CDIH)=19.481 E(NOE )=374.752 E(PLAN)=13.945 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64548 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64638 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64569 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 64579 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64530 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 64480 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64433 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64431 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64415 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=1745.739 E(kin)=621.817 temperature=308.136 | | Etotal =1123.922 grad(E)=63.690 E(BOND)=237.732 E(ANGL)=574.954 | | E(DIHE)=0.000 E(IMPR)=116.086 E(VDW )=-59.618 E(ELEC)=-139.182 | | E(CDIH)=19.129 E(NOE )=356.021 E(PLAN)=18.800 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 64383 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64347 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64310 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64264 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64291 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64331 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart NBONDS: found 64265 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 64268 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64232 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64226 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64203 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=1757.073 E(kin)=618.839 temperature=306.661 | | Etotal =1138.234 grad(E)=63.260 E(BOND)=258.142 E(ANGL)=560.387 | | E(DIHE)=0.000 E(IMPR)=138.007 E(VDW )=-70.378 E(ELEC)=-143.980 | | E(CDIH)=19.670 E(NOE )=355.438 E(PLAN)=20.947 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64177 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 64146 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 64099 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64104 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64147 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64198 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64125 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=1745.977 E(kin)=589.500 temperature=292.122 | | Etotal =1156.476 grad(E)=65.262 E(BOND)=257.020 E(ANGL)=547.091 | | E(DIHE)=0.000 E(IMPR)=151.238 E(VDW )=-53.464 E(ELEC)=-135.604 | | E(CDIH)=22.136 E(NOE )=348.562 E(PLAN)=19.497 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.50 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64176 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64154 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 64184 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64192 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64179 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64227 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=1748.913 E(kin)=613.848 temperature=304.188 | | Etotal =1135.065 grad(E)=65.347 E(BOND)=259.003 E(ANGL)=540.820 | | E(DIHE)=0.000 E(IMPR)=131.750 E(VDW )=-54.748 E(ELEC)=-135.623 | | E(CDIH)=16.267 E(NOE )=359.667 E(PLAN)=17.927 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1757.824 E(kin)=605.564 temperature=300.082 | | Etotal =1152.260 grad(E)=66.142 E(BOND)=254.211 E(ANGL)=560.597 | | E(DIHE)=0.000 E(IMPR)=131.692 E(VDW )=-63.419 E(ELEC)=-135.876 | | E(CDIH)=21.962 E(NOE )=365.731 E(PLAN)=17.363 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.674 E(kin)=12.313 temperature=6.102 | | Etotal =15.841 grad(E)=1.475 E(BOND)=11.913 E(ANGL)=15.549 | | E(DIHE)=0.000 E(IMPR)=8.636 E(VDW )=10.736 E(ELEC)=3.984 | | E(CDIH)=4.654 E(NOE )=12.155 E(PLAN)=2.747 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=1763.892 E(kin)=605.458 temperature=300.030 | | Etotal =1158.435 grad(E)=61.615 E(BOND)=240.239 E(ANGL)=563.127 | | E(DIHE)=0.000 E(IMPR)=127.901 E(VDW )=-55.173 E(ELEC)=-131.863 | | E(CDIH)=23.837 E(NOE )=372.302 E(PLAN)=18.066 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=81.402 E(kin)=12.853 temperature=6.369 | | Etotal =82.271 grad(E)=4.242 E(BOND)=24.478 E(ANGL)=55.207 | | E(DIHE)=0.000 E(IMPR)=11.028 E(VDW )=25.267 E(ELEC)=7.608 | | E(CDIH)=7.473 E(NOE )=23.529 E(PLAN)=3.237 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64264 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64278 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.32 A apart NBONDS: found 64329 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64367 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64426 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64482 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64529 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=1767.690 E(kin)=604.012 temperature=299.313 | | Etotal =1163.678 grad(E)=65.970 E(BOND)=235.690 E(ANGL)=598.337 | | E(DIHE)=0.000 E(IMPR)=126.607 E(VDW )=-75.770 E(ELEC)=-145.164 | | E(CDIH)=26.700 E(NOE )=378.766 E(PLAN)=18.511 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64608 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64649 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 64682 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64755 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64747 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64746 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=1767.935 E(kin)=600.881 temperature=297.762 | | Etotal =1167.054 grad(E)=66.907 E(BOND)=250.056 E(ANGL)=571.837 | | E(DIHE)=0.000 E(IMPR)=129.548 E(VDW )=-76.136 E(ELEC)=-137.842 | | E(CDIH)=23.601 E(NOE )=384.545 E(PLAN)=21.444 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64737 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64748 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64754 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64722 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64686 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64735 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=1758.788 E(kin)=597.614 temperature=296.143 | | Etotal =1161.174 grad(E)=66.731 E(BOND)=256.017 E(ANGL)=579.773 | | E(DIHE)=0.000 E(IMPR)=116.323 E(VDW )=-59.155 E(ELEC)=-139.707 | | E(CDIH)=19.544 E(NOE )=368.366 E(PLAN)=20.012 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 64766 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64782 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64889 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64916 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64993 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 65094 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=1764.930 E(kin)=587.789 temperature=291.274 | | Etotal =1177.141 grad(E)=67.735 E(BOND)=270.442 E(ANGL)=565.668 | | E(DIHE)=0.000 E(IMPR)=130.908 E(VDW )=-61.060 E(ELEC)=-136.419 | | E(CDIH)=23.710 E(NOE )=368.244 E(PLAN)=15.648 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65180 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65224 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65235 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 65219 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65231 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65237 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65266 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65237 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=1744.955 E(kin)=607.021 temperature=300.804 | | Etotal =1137.934 grad(E)=67.053 E(BOND)=245.310 E(ANGL)=563.915 | | E(DIHE)=0.000 E(IMPR)=132.815 E(VDW )=-81.271 E(ELEC)=-130.711 | | E(CDIH)=26.317 E(NOE )=365.261 E(PLAN)=16.299 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65262 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65247 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65212 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 65213 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 65249 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.30 A apart NBONDS: found 65270 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 65297 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65270 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65318 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=1737.634 E(kin)=593.178 temperature=293.945 | | Etotal =1144.455 grad(E)=66.006 E(BOND)=264.213 E(ANGL)=555.544 | | E(DIHE)=0.000 E(IMPR)=128.400 E(VDW )=-72.030 E(ELEC)=-149.389 | | E(CDIH)=19.973 E(NOE )=379.970 E(PLAN)=17.774 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65299 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65312 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65278 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65278 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65105 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=1735.273 E(kin)=631.486 temperature=312.928 | | Etotal =1103.788 grad(E)=63.886 E(BOND)=250.643 E(ANGL)=527.214 | | E(DIHE)=0.000 E(IMPR)=128.829 E(VDW )=-60.217 E(ELEC)=-145.037 | | E(CDIH)=29.713 E(NOE )=354.052 E(PLAN)=18.592 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64975 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64873 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 64825 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64720 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64652 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64628 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64646 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 64602 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart NBONDS: found 64631 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=1769.560 E(kin)=623.873 temperature=309.155 | | Etotal =1145.687 grad(E)=63.093 E(BOND)=267.545 E(ANGL)=548.249 | | E(DIHE)=0.000 E(IMPR)=124.431 E(VDW )=-65.926 E(ELEC)=-147.552 | | E(CDIH)=29.923 E(NOE )=370.508 E(PLAN)=18.510 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64666 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 64765 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 64873 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart NBONDS: found 64990 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65087 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65066 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=1746.443 E(kin)=591.482 temperature=293.104 | | Etotal =1154.961 grad(E)=65.354 E(BOND)=253.663 E(ANGL)=574.538 | | E(DIHE)=0.000 E(IMPR)=136.185 E(VDW )=-69.464 E(ELEC)=-142.585 | | E(CDIH)=25.586 E(NOE )=362.062 E(PLAN)=14.976 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65059 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65035 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65041 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65071 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65198 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65276 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65440 intra-atom interactions NBONDS: found 65467 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=1756.492 E(kin)=613.870 temperature=304.198 | | Etotal =1142.622 grad(E)=64.817 E(BOND)=248.347 E(ANGL)=551.537 | | E(DIHE)=0.000 E(IMPR)=136.465 E(VDW )=-61.637 E(ELEC)=-146.927 | | E(CDIH)=21.888 E(NOE )=376.654 E(PLAN)=16.295 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1757.644 E(kin)=605.460 temperature=300.031 | | Etotal =1152.184 grad(E)=66.366 E(BOND)=254.103 E(ANGL)=564.600 | | E(DIHE)=0.000 E(IMPR)=131.343 E(VDW )=-63.756 E(ELEC)=-140.782 | | E(CDIH)=22.982 E(NOE )=365.860 E(PLAN)=17.833 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.973 E(kin)=12.857 temperature=6.371 | | Etotal =16.446 grad(E)=1.418 E(BOND)=12.093 E(ANGL)=16.783 | | E(DIHE)=0.000 E(IMPR)=9.006 E(VDW )=11.148 E(ELEC)=5.648 | | E(CDIH)=5.057 E(NOE )=13.024 E(PLAN)=2.164 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=1763.411 E(kin)=605.458 temperature=300.030 | | Etotal =1157.954 grad(E)=61.980 E(BOND)=241.306 E(ANGL)=563.240 | | E(DIHE)=0.000 E(IMPR)=128.165 E(VDW )=-55.834 E(ELEC)=-132.549 | | E(CDIH)=23.771 E(NOE )=371.806 E(PLAN)=18.048 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=78.285 E(kin)=12.854 temperature=6.369 | | Etotal =79.193 grad(E)=4.286 E(BOND)=24.042 E(ANGL)=53.246 | | E(DIHE)=0.000 E(IMPR)=10.925 E(VDW )=24.578 E(ELEC)=7.844 | | E(CDIH)=7.319 E(NOE )=22.957 E(PLAN)=3.168 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.28 A apart NBONDS: found 65618 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.27 A apart NBONDS: found 65672 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65634 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65611 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65540 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=1748.248 E(kin)=604.009 temperature=299.312 | | Etotal =1144.238 grad(E)=65.449 E(BOND)=250.460 E(ANGL)=544.283 | | E(DIHE)=0.000 E(IMPR)=129.027 E(VDW )=-50.451 E(ELEC)=-138.976 | | E(CDIH)=15.920 E(NOE )=379.256 E(PLAN)=14.720 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65459 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65446 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart NBONDS: found 65387 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65368 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65284 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 65312 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart NBONDS: found 65345 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=1751.790 E(kin)=602.550 temperature=298.589 | | Etotal =1149.240 grad(E)=67.372 E(BOND)=267.836 E(ANGL)=558.342 | | E(DIHE)=0.000 E(IMPR)=124.034 E(VDW )=-67.233 E(ELEC)=-134.315 | | E(CDIH)=26.450 E(NOE )=356.931 E(PLAN)=17.194 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65324 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65394 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 65375 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65344 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 65253 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65234 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 65206 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=1741.151 E(kin)=623.093 temperature=308.769 | | Etotal =1118.058 grad(E)=64.268 E(BOND)=236.297 E(ANGL)=557.481 | | E(DIHE)=0.000 E(IMPR)=129.748 E(VDW )=-72.334 E(ELEC)=-137.805 | | E(CDIH)=27.165 E(NOE )=358.879 E(PLAN)=18.629 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65187 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65152 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65137 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65140 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65082 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65023 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64985 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64983 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64999 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=1769.492 E(kin)=602.113 temperature=298.372 | | Etotal =1167.379 grad(E)=67.649 E(BOND)=252.376 E(ANGL)=578.391 | | E(DIHE)=0.000 E(IMPR)=147.619 E(VDW )=-65.448 E(ELEC)=-128.124 | | E(CDIH)=19.393 E(NOE )=344.620 E(PLAN)=18.553 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65033 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65042 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H4' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65081 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65116 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65097 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65086 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65085 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65119 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65124 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=1769.669 E(kin)=600.106 temperature=297.378 | | Etotal =1169.563 grad(E)=65.228 E(BOND)=273.366 E(ANGL)=530.432 | | E(DIHE)=0.000 E(IMPR)=141.336 E(VDW )=-67.593 E(ELEC)=-134.893 | | E(CDIH)=27.357 E(NOE )=377.542 E(PLAN)=22.015 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65188 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65226 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65224 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65155 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65074 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64978 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=1767.113 E(kin)=603.700 temperature=299.159 | | Etotal =1163.413 grad(E)=66.617 E(BOND)=255.920 E(ANGL)=554.674 | | E(DIHE)=0.000 E(IMPR)=128.623 E(VDW )=-68.899 E(ELEC)=-131.197 | | E(CDIH)=24.830 E(NOE )=378.210 E(PLAN)=21.252 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64926 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64862 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64876 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 64859 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 64865 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64883 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64881 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64862 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64837 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.34 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64810 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64785 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=1755.393 E(kin)=592.680 temperature=293.698 | | Etotal =1162.713 grad(E)=66.384 E(BOND)=251.003 E(ANGL)=583.353 | | E(DIHE)=0.000 E(IMPR)=125.477 E(VDW )=-61.284 E(ELEC)=-138.608 | | E(CDIH)=17.474 E(NOE )=367.182 E(PLAN)=18.116 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64685 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64609 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64615 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64571 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64448 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64336 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=1766.499 E(kin)=591.129 temperature=292.929 | | Etotal =1175.370 grad(E)=65.473 E(BOND)=244.059 E(ANGL)=585.409 | | E(DIHE)=0.000 E(IMPR)=135.924 E(VDW )=-66.256 E(ELEC)=-135.950 | | E(CDIH)=25.990 E(NOE )=365.482 E(PLAN)=20.712 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64231 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64109 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64063 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64050 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64057 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64073 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 64059 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64046 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=1775.184 E(kin)=591.116 temperature=292.923 | | Etotal =1184.068 grad(E)=66.791 E(BOND)=267.596 E(ANGL)=582.925 | | E(DIHE)=0.000 E(IMPR)=117.595 E(VDW )=-56.603 E(ELEC)=-135.289 | | E(CDIH)=27.322 E(NOE )=360.831 E(PLAN)=19.691 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64052 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64120 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64073 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64054 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64060 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 64117 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 64119 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=1765.902 E(kin)=607.005 temperature=300.797 | | Etotal =1158.897 grad(E)=65.354 E(BOND)=252.107 E(ANGL)=563.397 | | E(DIHE)=0.000 E(IMPR)=151.553 E(VDW )=-72.970 E(ELEC)=-124.580 | | E(CDIH)=19.292 E(NOE )=354.821 E(PLAN)=15.277 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1757.454 E(kin)=605.449 temperature=300.025 | | Etotal =1152.005 grad(E)=65.537 E(BOND)=253.123 E(ANGL)=560.439 | | E(DIHE)=0.000 E(IMPR)=132.800 E(VDW )=-62.888 E(ELEC)=-135.605 | | E(CDIH)=22.351 E(NOE )=364.374 E(PLAN)=17.411 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.623 E(kin)=12.543 temperature=6.216 | | Etotal =16.019 grad(E)=1.312 E(BOND)=11.593 E(ANGL)=15.987 | | E(DIHE)=0.000 E(IMPR)=9.122 E(VDW )=10.889 E(ELEC)=4.094 | | E(CDIH)=4.588 E(NOE )=13.854 E(PLAN)=2.172 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=1762.986 E(kin)=605.457 temperature=300.029 | | Etotal =1157.529 grad(E)=62.234 E(BOND)=242.150 E(ANGL)=563.040 | | E(DIHE)=0.000 E(IMPR)=128.496 E(VDW )=-56.338 E(ELEC)=-132.768 | | E(CDIH)=23.670 E(NOE )=371.275 E(PLAN)=18.002 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=75.507 E(kin)=12.832 temperature=6.359 | | Etotal =76.447 grad(E)=4.245 E(BOND)=23.571 E(ANGL)=51.492 | | E(DIHE)=0.000 E(IMPR)=10.871 E(VDW )=23.931 E(ELEC)=7.678 | | E(CDIH)=7.168 E(NOE )=22.512 E(PLAN)=3.112 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64269 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64318 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64330 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64399 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -10 -CYT -H41 " only 1.45 A apart %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64474 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64573 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 64640 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=1766.784 E(kin)=599.702 temperature=297.177 | | Etotal =1167.083 grad(E)=65.687 E(BOND)=262.890 E(ANGL)=608.347 | | E(DIHE)=0.000 E(IMPR)=126.944 E(VDW )=-85.154 E(ELEC)=-124.413 | | E(CDIH)=25.038 E(NOE )=332.024 E(PLAN)=21.408 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 64701 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64746 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 64774 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 64727 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64693 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64627 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64530 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=1757.981 E(kin)=589.831 temperature=292.286 | | Etotal =1168.150 grad(E)=67.975 E(BOND)=267.350 E(ANGL)=558.003 | | E(DIHE)=0.000 E(IMPR)=137.259 E(VDW )=-70.128 E(ELEC)=-134.773 | | E(CDIH)=18.891 E(NOE )=374.413 E(PLAN)=17.136 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64500 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64428 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.50 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64336 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64315 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64257 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64204 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64197 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=1745.035 E(kin)=611.525 temperature=303.036 | | Etotal =1133.510 grad(E)=64.304 E(BOND)=250.482 E(ANGL)=553.736 | | E(DIHE)=0.000 E(IMPR)=137.245 E(VDW )=-61.267 E(ELEC)=-141.766 | | E(CDIH)=21.364 E(NOE )=357.245 E(PLAN)=16.470 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64231 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64247 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64360 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64467 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64545 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64567 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=1772.460 E(kin)=619.420 temperature=306.949 | | Etotal =1153.039 grad(E)=64.895 E(BOND)=242.776 E(ANGL)=557.462 | | E(DIHE)=0.000 E(IMPR)=126.362 E(VDW )=-73.951 E(ELEC)=-143.055 | | E(CDIH)=36.631 E(NOE )=391.517 E(PLAN)=15.298 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64623 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64675 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64718 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64796 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64826 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64830 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=1750.741 E(kin)=606.499 temperature=300.545 | | Etotal =1144.242 grad(E)=63.983 E(BOND)=244.591 E(ANGL)=565.588 | | E(DIHE)=0.000 E(IMPR)=132.422 E(VDW )=-68.240 E(ELEC)=-140.637 | | E(CDIH)=22.297 E(NOE )=372.944 E(PLAN)=15.279 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64872 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64939 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65001 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65098 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65189 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65284 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 65369 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=1767.562 E(kin)=618.913 temperature=306.698 | | Etotal =1148.649 grad(E)=65.828 E(BOND)=242.071 E(ANGL)=571.342 | | E(DIHE)=0.000 E(IMPR)=126.884 E(VDW )=-61.038 E(ELEC)=-139.303 | | E(CDIH)=16.028 E(NOE )=375.079 E(PLAN)=17.587 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65380 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65460 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65510 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65512 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 65459 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 65457 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65394 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65400 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=1739.337 E(kin)=591.100 temperature=292.915 | | Etotal =1148.237 grad(E)=65.570 E(BOND)=270.300 E(ANGL)=560.523 | | E(DIHE)=0.000 E(IMPR)=133.137 E(VDW )=-74.588 E(ELEC)=-140.316 | | E(CDIH)=18.839 E(NOE )=364.475 E(PLAN)=15.867 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart NBONDS: found 65376 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65393 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart NBONDS: found 65323 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65331 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65232 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=1755.116 E(kin)=606.748 temperature=300.669 | | Etotal =1148.368 grad(E)=65.896 E(BOND)=239.447 E(ANGL)=618.078 | | E(DIHE)=0.000 E(IMPR)=127.016 E(VDW )=-83.804 E(ELEC)=-138.713 | | E(CDIH)=24.328 E(NOE )=343.156 E(PLAN)=18.860 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65330 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65361 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65444 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65498 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65549 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 65548 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65551 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=1761.854 E(kin)=624.623 temperature=309.527 | | Etotal =1137.231 grad(E)=65.128 E(BOND)=245.461 E(ANGL)=566.156 | | E(DIHE)=0.000 E(IMPR)=115.794 E(VDW )=-76.291 E(ELEC)=-133.051 | | E(CDIH)=23.539 E(NOE )=377.691 E(PLAN)=17.932 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65516 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65525 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65576 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.37 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65578 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65622 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65621 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart NBONDS: found 65656 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=1742.373 E(kin)=601.104 temperature=297.872 | | Etotal =1141.269 grad(E)=65.648 E(BOND)=239.680 E(ANGL)=551.464 | | E(DIHE)=0.000 E(IMPR)=138.398 E(VDW )=-52.106 E(ELEC)=-139.425 | | E(CDIH)=30.981 E(NOE )=354.596 E(PLAN)=17.680 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1760.178 E(kin)=605.556 temperature=300.079 | | Etotal =1154.621 grad(E)=65.392 E(BOND)=254.534 E(ANGL)=568.912 | | E(DIHE)=0.000 E(IMPR)=128.573 E(VDW )=-65.112 E(ELEC)=-136.583 | | E(CDIH)=22.343 E(NOE )=364.260 E(PLAN)=17.693 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.220 E(kin)=12.358 temperature=6.124 | | Etotal =15.599 grad(E)=1.310 E(BOND)=12.262 E(ANGL)=16.918 | | E(DIHE)=0.000 E(IMPR)=8.613 E(VDW )=11.339 E(ELEC)=5.360 | | E(CDIH)=4.878 E(NOE )=15.145 E(PLAN)=2.491 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=1762.799 E(kin)=605.464 temperature=300.033 | | Etotal =1157.335 grad(E)=62.445 E(BOND)=242.976 E(ANGL)=563.432 | | E(DIHE)=0.000 E(IMPR)=128.502 E(VDW )=-56.922 E(ELEC)=-133.022 | | E(CDIH)=23.581 E(NOE )=370.808 E(PLAN)=17.982 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=72.997 E(kin)=12.801 temperature=6.343 | | Etotal =73.968 grad(E)=4.190 E(BOND)=23.197 E(ANGL)=49.959 | | E(DIHE)=0.000 E(IMPR)=10.736 E(VDW )=23.407 E(ELEC)=7.605 | | E(CDIH)=7.046 E(NOE )=22.166 E(PLAN)=3.075 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65648 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65620 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65545 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart NBONDS: found 65537 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65531 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65516 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65476 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart NBONDS: found 65483 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65469 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=1751.674 E(kin)=596.603 temperature=295.642 | | Etotal =1155.071 grad(E)=67.105 E(BOND)=245.540 E(ANGL)=568.055 | | E(DIHE)=0.000 E(IMPR)=154.943 E(VDW )=-65.158 E(ELEC)=-144.289 | | E(CDIH)=21.096 E(NOE )=357.565 E(PLAN)=17.321 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65469 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65470 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65506 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65537 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65579 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65576 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=1745.772 E(kin)=628.322 temperature=311.360 | | Etotal =1117.450 grad(E)=66.056 E(BOND)=239.960 E(ANGL)=575.650 | | E(DIHE)=0.000 E(IMPR)=135.145 E(VDW )=-63.755 E(ELEC)=-142.282 | | E(CDIH)=21.788 E(NOE )=337.603 E(PLAN)=13.341 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 65625 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65672 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65782 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65832 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 65865 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65945 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 66000 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H4' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65994 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=1770.178 E(kin)=610.405 temperature=302.481 | | Etotal =1159.773 grad(E)=67.463 E(BOND)=253.974 E(ANGL)=549.796 | | E(DIHE)=0.000 E(IMPR)=141.123 E(VDW )=-49.818 E(ELEC)=-147.913 | | E(CDIH)=21.304 E(NOE )=375.177 E(PLAN)=16.130 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -12 -URI -H5''" only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65976 intra-atom interactions %atoms "A -8 -CYT -O5' " and "A -8 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65892 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65798 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 65742 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65623 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65431 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart NBONDS: found 65407 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=1765.510 E(kin)=601.150 temperature=297.895 | | Etotal =1164.360 grad(E)=68.389 E(BOND)=257.891 E(ANGL)=561.337 | | E(DIHE)=0.000 E(IMPR)=162.728 E(VDW )=-72.227 E(ELEC)=-147.925 | | E(CDIH)=16.324 E(NOE )=371.985 E(PLAN)=14.247 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65350 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart NBONDS: found 65332 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart NBONDS: found 65281 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65248 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart NBONDS: found 65234 intra-atom interactions NBONDS: found 65245 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.49 A apart NBONDS: found 65278 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65309 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=1746.355 E(kin)=602.150 temperature=298.391 | | Etotal =1144.205 grad(E)=66.114 E(BOND)=236.199 E(ANGL)=580.915 | | E(DIHE)=0.000 E(IMPR)=143.217 E(VDW )=-72.040 E(ELEC)=-138.492 | | E(CDIH)=30.738 E(NOE )=347.938 E(PLAN)=15.729 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65305 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.38 A apart NBONDS: found 65279 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.45 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65222 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65168 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65106 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65031 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.36 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64947 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64870 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=1745.310 E(kin)=622.809 temperature=308.628 | | Etotal =1122.500 grad(E)=64.611 E(BOND)=258.423 E(ANGL)=553.145 | | E(DIHE)=0.000 E(IMPR)=133.582 E(VDW )=-69.129 E(ELEC)=-140.826 | | E(CDIH)=19.306 E(NOE )=352.299 E(PLAN)=15.701 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64778 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64731 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64718 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64703 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64712 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 64702 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 64747 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64703 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=1762.268 E(kin)=600.898 temperature=297.770 | | Etotal =1161.370 grad(E)=68.381 E(BOND)=244.550 E(ANGL)=577.539 | | E(DIHE)=0.000 E(IMPR)=131.630 E(VDW )=-68.921 E(ELEC)=-146.911 | | E(CDIH)=21.665 E(NOE )=381.799 E(PLAN)=20.019 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64719 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64763 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64753 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64704 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.44 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64555 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64505 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64412 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.39 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64302 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=1756.687 E(kin)=588.162 temperature=291.459 | | Etotal =1168.525 grad(E)=66.890 E(BOND)=260.652 E(ANGL)=584.924 | | E(DIHE)=0.000 E(IMPR)=138.459 E(VDW )=-56.906 E(ELEC)=-150.931 | | E(CDIH)=26.106 E(NOE )=348.066 E(PLAN)=18.157 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.40 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64285 intra-atom interactions %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64160 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64104 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64100 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64136 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64157 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64231 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=1765.340 E(kin)=601.967 temperature=298.300 | | Etotal =1163.373 grad(E)=70.127 E(BOND)=265.572 E(ANGL)=554.746 | | E(DIHE)=0.000 E(IMPR)=114.967 E(VDW )=-44.398 E(ELEC)=-149.409 | | E(CDIH)=19.590 E(NOE )=384.255 E(PLAN)=18.050 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64308 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64409 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64570 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.46 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64745 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.47 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64862 intra-atom interactions %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 64934 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=1756.809 E(kin)=580.590 temperature=287.707 | | Etotal =1176.219 grad(E)=68.610 E(BOND)=255.263 E(ANGL)=590.881 | | E(DIHE)=0.000 E(IMPR)=149.072 E(VDW )=-61.398 E(ELEC)=-144.665 | | E(CDIH)=23.295 E(NOE )=347.691 E(PLAN)=16.080 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1755.562 E(kin)=605.417 temperature=300.009 | | Etotal =1150.145 grad(E)=67.113 E(BOND)=252.432 E(ANGL)=569.185 | | E(DIHE)=0.000 E(IMPR)=133.246 E(VDW )=-64.380 E(ELEC)=-144.019 | | E(CDIH)=22.281 E(NOE )=363.883 E(PLAN)=17.516 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.542 E(kin)=12.755 temperature=6.321 | | Etotal =15.512 grad(E)=1.402 E(BOND)=11.888 E(ANGL)=16.676 | | E(DIHE)=0.000 E(IMPR)=8.687 E(VDW )=12.414 E(ELEC)=4.490 | | E(CDIH)=5.284 E(NOE )=14.453 E(PLAN)=2.427 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=1762.346 E(kin)=605.461 temperature=300.031 | | Etotal =1156.886 grad(E)=62.736 E(BOND)=243.567 E(ANGL)=563.791 | | E(DIHE)=0.000 E(IMPR)=128.798 E(VDW )=-57.389 E(ELEC)=-133.709 | | E(CDIH)=23.500 E(NOE )=370.375 E(PLAN)=17.953 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=70.741 E(kin)=12.798 temperature=6.342 | | Etotal =71.746 grad(E)=4.226 E(BOND)=22.772 E(ANGL)=48.572 | | E(DIHE)=0.000 E(IMPR)=10.681 E(VDW )=22.946 E(ELEC)=7.910 | | E(CDIH)=6.956 E(NOE )=21.829 E(PLAN)=3.041 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.07349 0.03457 -0.00585 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR>close refine.tra end %X-PLOR>-ERR: File refine.tra was not open. X-PLOR> X-PLOR>! Compute dynamics average over second half of trajectory. X-PLOR> X-PLOR>evaluate ($steps2=$steps/2) EVALUATE: symbol $STEPS2 set to 20000.0 (real) X-PLOR>dynamics analysis average AVECOR> input=refine.tra ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.tra opened. AVECOR> begin=$steps2 AVECOR> skip=200 AVECOR> stop=$steps AVECOR>end REMARKS FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.tra" REMARKS DATE:17-Aug-96 02:51:43 created by user: READC: reading file= 1 ISTART= 200 READC: 677 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 20000 SKIP= 200 STOP= 40000 READC: TIMEstep= 0.00050000 ps header= CORD READC: complete. 101 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR>close refine.tra end ! disposition=delete doesn't work X-PLOR> X-PLOR>! Final minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.42 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65070 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65072 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H3' " and "A -12 -URI -O5' " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65058 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =584.366 grad(E)=9.324 E(BOND)=53.855 E(ANGL)=323.629 | | E(DIHE)=0.000 E(IMPR)=53.614 E(VDW )=-54.331 E(ELEC)=-142.992 | | E(CDIH)=19.510 E(NOE )=315.767 E(PLAN)=15.314 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =556.429 grad(E)=2.674 E(BOND)=48.228 E(ANGL)=308.614 | | E(DIHE)=0.000 E(IMPR)=54.266 E(VDW )=-70.698 E(ELEC)=-142.855 | | E(CDIH)=19.316 E(NOE )=325.077 E(PLAN)=14.480 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =551.078 grad(E)=1.645 E(BOND)=48.697 E(ANGL)=303.917 | | E(DIHE)=0.000 E(IMPR)=54.267 E(VDW )=-79.537 E(ELEC)=-144.515 | | E(CDIH)=19.529 E(NOE )=335.477 E(PLAN)=13.242 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =548.756 grad(E)=1.040 E(BOND)=48.351 E(ANGL)=302.675 | | E(DIHE)=0.000 E(IMPR)=54.122 E(VDW )=-78.541 E(ELEC)=-146.610 | | E(CDIH)=19.953 E(NOE )=336.223 E(PLAN)=12.584 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =547.232 grad(E)=1.201 E(BOND)=48.281 E(ANGL)=303.538 | | E(DIHE)=0.000 E(IMPR)=54.333 E(VDW )=-77.821 E(ELEC)=-148.169 | | E(CDIH)=19.939 E(NOE )=334.927 E(PLAN)=12.205 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =545.725 grad(E)=1.835 E(BOND)=48.221 E(ANGL)=304.098 | | E(DIHE)=0.000 E(IMPR)=54.255 E(VDW )=-77.465 E(ELEC)=-149.572 | | E(CDIH)=19.785 E(NOE )=334.285 E(PLAN)=12.118 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =544.512 grad(E)=1.105 E(BOND)=48.114 E(ANGL)=303.066 | | E(DIHE)=0.000 E(IMPR)=54.032 E(VDW )=-76.853 E(ELEC)=-150.610 | | E(CDIH)=19.973 E(NOE )=334.546 E(PLAN)=12.245 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =543.531 grad(E)=0.808 E(BOND)=47.909 E(ANGL)=302.448 | | E(DIHE)=0.000 E(IMPR)=53.764 E(VDW )=-76.829 E(ELEC)=-151.636 | | E(CDIH)=20.030 E(NOE )=335.551 E(PLAN)=12.294 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Analyze and write out the final structure. X-PLOR> X-PLOR>print threshold=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. (A 11 C8 |A 11 H8 ) 1.130 1.080 0.050 5.034 2000.000 (A 12 N1 |A 12 C6 ) 1.316 1.375 -0.059 4.831 1370.370 Number of violations greater 0.050: 2 RMS deviation= 0.006 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.559560E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 2.00000 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (A 10 C5' |A 10 C4' |A 10 C3' ) 122.534 115.500 7.034 7.368 488.878 (A 10 C1' |A 10 C2' |A 10 O2' ) 105.575 110.600 -5.025 2.752 357.719 (A 11 O4' |A 11 C4' |A 11 C3' ) 93.990 105.500 -11.510 22.648 561.212 (A 11 C4' |A 11 C3' |A 11 O3' ) 123.640 110.500 13.140 23.405 445.032 (A 11 O4' |A 11 C1' |A 11 N9 ) 115.080 108.200 6.880 15.859 1099.976 (A 11 N9 |A 11 C1' |A 11 C2' ) 99.489 113.400 -13.911 25.329 429.678 (A 12 C5' |A 12 C4' |A 12 C3' ) 123.096 115.500 7.596 8.593 488.878 (A 12 O4' |A 12 C1' |A 12 C2' ) 100.275 106.400 -6.125 6.413 561.212 (A 12 C1' |A 12 N1 |A 12 C6 ) 114.838 121.200 -6.362 6.918 561.212 Number of violations greater 5.000: 9 RMS deviation= 1.123 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 1.12278 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 9.00000 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period (A 11 C1' |A 11 C4 |A 11 C8 |A 11 N9 ) -5.550 0.000 5.550 22.523 2400.000 0 Number of violations greater 5.000: 1 RMS deviation= 0.667 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.666547 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 1.00000 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 9 URI H2' set-j-atoms A 10 CYT H6 R= 5.444 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.444 E(NOE)= 19.733 ======================================== set-i-atoms A 9 URI H2' set-j-atoms A 11 ADE H8 R= 4.504 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.504 E(NOE)= 25.401 ======================================== set-i-atoms A 10 CYT H1' set-j-atoms A 11 ADE H8 R= 5.912 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.912 E(NOE)= 83.138 ======================================== set-i-atoms A 10 CYT H4' set-j-atoms A 11 ADE H8 R= 5.646 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.646 E(NOE)= 41.775 ======================================== set-i-atoms A 11 ADE H2 set-j-atoms A 12 URI H1' R= 5.362 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.362 E(NOE)= 13.074 ======================================== set-i-atoms A 11 ADE H8 set-j-atoms A 12 URI H6 R= 2.779 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.221 E(NOE)= 4.898 ======================================== set-i-atoms A 11 ADE H2' set-j-atoms A 12 URI H6 R= 4.769 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.769 E(NOE)= 59.196 ======================================== set-i-atoms A 11 ADE H3' set-j-atoms A 12 URI H6 R= 2.763 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.237 E(NOE)= 5.627 ======================================== set-i-atoms A 12 URI H6 set-j-atoms A 12 URI H3' R= 4.355 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.355 E(NOE)= 12.625 ======================================== set-i-atoms A 12 URI H1' set-j-atoms A 12 URI H4' R= 2.724 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.276 E(NOE)= 7.617 ======================================== set-i-atoms A 12 URI H2' set-j-atoms A 13 ADE H8 R= 2.699 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.301 E(NOE)= 9.076 ======================================== set-i-atoms A 12 URI H6 set-j-atoms A 13 ADE H8 R= 5.569 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.569 E(NOE)= 32.324 NOEPRI: RMS diff. = 0.060, #(violat.> 0.2)= 12 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.060, #(viol.> 0.2)= 12 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.601319E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 12.0000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 ======================================== A 11 ADE O4' A 11 ADE C1' A 11 ADE N9 A 11 ADE C4 Dihedral= -121.332 Energy= 0.014 C= 1.000 Equil= -158.000 Delta= -6.668 Range= 30.000 Exponent= 2 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 1 RMS deviation= 0.636 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.636313 (real) X-PLOR>evaluate ($v_cdih=$violations) EVALUATE: symbol $V_CDIH set to 1.00000 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 47.9089, angle 302.448, dihedral 0, improper 53.7644, NOE 335.551, c-dihedral 20.0301, planar 12.2942, VdW -76.8289, elec -151.636, total 543.531 RMSD: bond 5.595598E-03, angle 1.12278, dihedral 0, improper 0.666547, NOE 6.013195E-02, c-dihedral 0.636313 Violations: bond 2, angle 9, dihedral 0, improper 1, NOE 12, c-dihedral 1 X-PLOR> X-PLOR>write coordinates output=refine.pdb end ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.pdb opened. X-PLOR> X-PLOR>stop CSTACK: size= 200000 used= 227 current= 0 HEAP: maximum use= 136482 current use= 0 X-PLOR: total CPU time= 2943.8376 s X-PLOR: entry time at 02:51:12 17-Aug-96 X-PLOR: exit time at 03:40:30 17-Aug-96