X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 04:33:06 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=19906.0414123535 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 18:49:59 created by user: COOR>ATOM 1 P GUA A 1 6.743 -9.563 3.100 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 6.719 -8.884 1.779 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 -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 63485 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =47.181 grad(E)=3.724 E(BOND)=16.225 E(ANGL)=160.972 | | E(DIHE)=0.000 E(IMPR)=21.169 E(VDW )=-206.202 E(ELEC)=-96.544 | | E(CDIH)=17.461 E(NOE )=124.320 E(PLAN)=9.781 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =34.643 grad(E)=2.197 E(BOND)=14.841 E(ANGL)=161.210 | | E(DIHE)=0.000 E(IMPR)=18.483 E(VDW )=-216.137 E(ELEC)=-98.516 | | E(CDIH)=16.816 E(NOE )=126.899 E(PLAN)=11.047 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =24.806 grad(E)=3.593 E(BOND)=14.328 E(ANGL)=158.185 | | E(DIHE)=0.000 E(IMPR)=19.294 E(VDW )=-215.995 E(ELEC)=-102.831 | | E(CDIH)=17.733 E(NOE )=122.705 E(PLAN)=11.387 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =15.958 grad(E)=2.915 E(BOND)=13.471 E(ANGL)=153.931 | | E(DIHE)=0.000 E(IMPR)=19.536 E(VDW )=-214.862 E(ELEC)=-109.307 | | E(CDIH)=17.570 E(NOE )=124.015 E(PLAN)=11.604 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =10.184 grad(E)=2.410 E(BOND)=14.873 E(ANGL)=153.413 | | E(DIHE)=0.000 E(IMPR)=19.851 E(VDW )=-216.112 E(ELEC)=-114.333 | | E(CDIH)=17.044 E(NOE )=124.104 E(PLAN)=11.343 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =4.571 grad(E)=3.202 E(BOND)=15.130 E(ANGL)=152.510 | | E(DIHE)=0.000 E(IMPR)=19.292 E(VDW )=-216.181 E(ELEC)=-120.753 | | E(CDIH)=16.489 E(NOE )=126.560 E(PLAN)=11.523 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63832 intra-atom interactions --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =0.425 grad(E)=1.740 E(BOND)=14.839 E(ANGL)=150.584 | | E(DIHE)=0.000 E(IMPR)=18.906 E(VDW )=-212.803 E(ELEC)=-125.553 | | E(CDIH)=16.020 E(NOE )=127.144 E(PLAN)=11.287 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =-2.362 grad(E)=1.031 E(BOND)=14.856 E(ANGL)=149.192 | | E(DIHE)=0.000 E(IMPR)=19.185 E(VDW )=-212.849 E(ELEC)=-129.866 | | E(CDIH)=15.911 E(NOE )=129.791 E(PLAN)=11.418 | ------------------------------------------------------------------------------- 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= 0.104135956E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : -0.09840 -0.02551 0.00097 velocity [A/ps] : -0.03815 -0.01148 0.17166 ang. mom. [amu A/ps] : 2807.28921 -9359.20665 -24652.48213 kin. ener. [Kcal/mol] : 0.25031 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : -0.09840 -0.02551 0.00097 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)=560.609 E(kin)=562.971 temperature=278.976 | | Etotal =-2.362 grad(E)=1.031 E(BOND)=14.856 E(ANGL)=149.192 | | E(DIHE)=0.000 E(IMPR)=19.185 E(VDW )=-212.849 E(ELEC)=-129.866 | | E(CDIH)=15.911 E(NOE )=129.791 E(PLAN)=11.418 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63904 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63880 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63913 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63870 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5''" only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63834 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63812 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63778 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63790 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63784 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5''" only 1.50 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63808 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=1209.673 E(kin)=597.668 temperature=296.170 | | Etotal =612.005 grad(E)=66.819 E(BOND)=212.953 E(ANGL)=418.689 | | E(DIHE)=0.000 E(IMPR)=85.841 E(VDW )=-197.990 E(ELEC)=-112.609 | | E(CDIH)=24.972 E(NOE )=161.064 E(PLAN)=19.084 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5''" only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63812 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5''" only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63805 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5''" only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63849 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5''" only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63964 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5''" only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64010 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5''" only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64031 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64087 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64023 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=1173.060 E(kin)=578.919 temperature=286.879 | | Etotal =594.141 grad(E)=65.732 E(BOND)=218.331 E(ANGL)=398.471 | | E(DIHE)=0.000 E(IMPR)=107.249 E(VDW )=-200.393 E(ELEC)=-129.733 | | E(CDIH)=13.455 E(NOE )=166.807 E(PLAN)=19.955 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63978 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63896 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63905 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63841 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63805 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63730 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63628 intra-atom interactions %atoms "A -12 -URI -O3' " 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 63605 intra-atom interactions %atoms "A -12 -URI -O3' " 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 63649 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=1176.138 E(kin)=623.505 temperature=308.973 | | Etotal =552.634 grad(E)=62.024 E(BOND)=203.037 E(ANGL)=393.678 | | E(DIHE)=0.000 E(IMPR)=88.887 E(VDW )=-196.762 E(ELEC)=-130.037 | | E(CDIH)=20.422 E(NOE )=151.862 E(PLAN)=21.546 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63657 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63671 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63677 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63710 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63813 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63899 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63936 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63926 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63892 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63902 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=1157.676 E(kin)=585.576 temperature=290.178 | | Etotal =572.100 grad(E)=64.971 E(BOND)=202.120 E(ANGL)=424.662 | | E(DIHE)=0.000 E(IMPR)=106.815 E(VDW )=-202.805 E(ELEC)=-130.104 | | E(CDIH)=12.517 E(NOE )=142.332 E(PLAN)=16.564 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " 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 63878 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " 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 63833 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " 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 63783 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63766 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -12 -URI -O3' " 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 63726 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63639 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 -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63508 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=1166.210 E(kin)=586.087 temperature=290.431 | | Etotal =580.123 grad(E)=66.480 E(BOND)=226.760 E(ANGL)=416.958 | | E(DIHE)=0.000 E(IMPR)=98.513 E(VDW )=-213.915 E(ELEC)=-135.100 | | E(CDIH)=18.567 E(NOE )=152.747 E(PLAN)=15.592 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63477 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63417 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63430 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 -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63444 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 63459 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 63461 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63462 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=1148.344 E(kin)=598.336 temperature=296.501 | | Etotal =550.008 grad(E)=63.949 E(BOND)=210.672 E(ANGL)=413.015 | | E(DIHE)=0.000 E(IMPR)=97.015 E(VDW )=-220.253 E(ELEC)=-126.303 | | E(CDIH)=16.691 E(NOE )=142.343 E(PLAN)=16.828 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63547 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63561 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63578 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63563 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63582 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63566 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63613 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63621 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63551 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63566 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63593 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=1132.767 E(kin)=625.257 temperature=309.841 | | Etotal =507.510 grad(E)=63.808 E(BOND)=198.530 E(ANGL)=389.365 | | E(DIHE)=0.000 E(IMPR)=94.288 E(VDW )=-207.472 E(ELEC)=-139.724 | | E(CDIH)=16.757 E(NOE )=138.406 E(PLAN)=17.360 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63601 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63590 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63520 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63470 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63472 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63476 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " 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 63495 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63500 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63523 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63552 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63539 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " 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 63561 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=1141.284 E(kin)=618.088 temperature=306.289 | | Etotal =523.196 grad(E)=64.231 E(BOND)=217.057 E(ANGL)=394.847 | | E(DIHE)=0.000 E(IMPR)=96.850 E(VDW )=-217.576 E(ELEC)=-134.050 | | E(CDIH)=23.005 E(NOE )=124.270 E(PLAN)=18.792 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63577 intra-atom interactions %atoms "A -12 -URI -O3' " 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 63561 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63565 intra-atom interactions %atoms "A -12 -URI -O3' " 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 63587 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63534 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " 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 63468 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63387 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63317 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63254 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=1121.390 E(kin)=605.882 temperature=300.240 | | Etotal =515.508 grad(E)=63.649 E(BOND)=192.102 E(ANGL)=406.942 | | E(DIHE)=0.000 E(IMPR)=100.281 E(VDW )=-224.343 E(ELEC)=-125.838 | | E(CDIH)=15.960 E(NOE )=135.322 E(PLAN)=15.083 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63172 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63099 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63077 intra-atom interactions %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63054 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63036 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63059 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63092 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63110 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63165 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63215 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=1121.624 E(kin)=594.738 temperature=294.718 | | Etotal =526.886 grad(E)=66.794 E(BOND)=210.628 E(ANGL)=399.765 | | E(DIHE)=0.000 E(IMPR)=99.616 E(VDW )=-212.050 E(ELEC)=-133.445 | | E(CDIH)=19.563 E(NOE )=127.276 E(PLAN)=15.533 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1149.414 E(kin)=603.377 temperature=298.999 | | Etotal =546.037 grad(E)=63.982 E(BOND)=209.475 E(ANGL)=398.500 | | E(DIHE)=0.000 E(IMPR)=93.132 E(VDW )=-208.949 E(ELEC)=-129.579 | | E(CDIH)=19.067 E(NOE )=146.961 E(PLAN)=17.432 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=46.214 E(kin)=22.360 temperature=11.080 | | Etotal =35.794 grad(E)=1.856 E(BOND)=13.117 E(ANGL)=17.097 | | E(DIHE)=0.000 E(IMPR)=7.515 E(VDW )=11.219 E(ELEC)=6.867 | | E(CDIH)=4.797 E(NOE )=13.493 E(PLAN)=2.449 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63311 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 -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63387 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63417 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63472 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63526 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 -11 -ADE -H5' " only 1.33 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63573 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " 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 63606 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart NBONDS: found 63692 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63763 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=1134.873 E(kin)=595.092 temperature=294.893 | | Etotal =539.781 grad(E)=65.447 E(BOND)=204.178 E(ANGL)=422.086 | | E(DIHE)=0.000 E(IMPR)=83.823 E(VDW )=-212.771 E(ELEC)=-123.956 | | E(CDIH)=28.473 E(NOE )=121.583 E(PLAN)=16.365 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63797 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63889 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63959 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63963 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63994 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.21 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63925 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63863 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 63779 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=1133.709 E(kin)=591.391 temperature=293.059 | | Etotal =542.318 grad(E)=64.926 E(BOND)=200.017 E(ANGL)=419.990 | | E(DIHE)=0.000 E(IMPR)=95.359 E(VDW )=-238.799 E(ELEC)=-131.854 | | E(CDIH)=21.296 E(NOE )=158.735 E(PLAN)=17.574 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63750 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63738 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63797 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63829 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63834 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63830 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 -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63824 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63826 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63797 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=1136.777 E(kin)=610.366 temperature=302.462 | | Etotal =526.411 grad(E)=62.627 E(BOND)=209.328 E(ANGL)=380.628 | | E(DIHE)=0.000 E(IMPR)=105.516 E(VDW )=-221.885 E(ELEC)=-127.327 | | E(CDIH)=22.034 E(NOE )=142.060 E(PLAN)=16.056 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63741 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63730 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63678 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63639 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63715 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63658 intra-atom interactions %atoms "A -9 -URI -H5' " and "A -10 -CYT -HO2'" only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63612 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63539 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=1120.744 E(kin)=601.074 temperature=297.857 | | Etotal =519.670 grad(E)=62.831 E(BOND)=212.520 E(ANGL)=388.830 | | E(DIHE)=0.000 E(IMPR)=86.124 E(VDW )=-231.469 E(ELEC)=-124.252 | | E(CDIH)=23.018 E(NOE )=149.361 E(PLAN)=15.538 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63508 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63461 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63394 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63322 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63318 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 63188 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63069 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 62914 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=1122.103 E(kin)=608.240 temperature=301.408 | | Etotal =513.864 grad(E)=65.232 E(BOND)=210.410 E(ANGL)=400.529 | | E(DIHE)=0.000 E(IMPR)=98.933 E(VDW )=-215.069 E(ELEC)=-137.001 | | E(CDIH)=22.925 E(NOE )=119.228 E(PLAN)=13.908 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62685 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 62622 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62568 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62563 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62480 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=1141.168 E(kin)=604.328 temperature=299.470 | | Etotal =536.840 grad(E)=64.207 E(BOND)=206.719 E(ANGL)=420.703 | | E(DIHE)=0.000 E(IMPR)=92.810 E(VDW )=-217.355 E(ELEC)=-136.941 | | E(CDIH)=13.346 E(NOE )=139.137 E(PLAN)=18.422 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62500 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.42 A apart NBONDS: found 62440 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62427 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62375 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62410 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62365 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=1150.744 E(kin)=610.250 temperature=302.404 | | Etotal =540.494 grad(E)=63.698 E(BOND)=212.191 E(ANGL)=400.114 | | E(DIHE)=0.000 E(IMPR)=88.672 E(VDW )=-219.854 E(ELEC)=-137.630 | | E(CDIH)=24.438 E(NOE )=153.753 E(PLAN)=18.811 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62305 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62287 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62166 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -12 -URI -O3' " 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 62067 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62019 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61899 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=1141.964 E(kin)=598.536 temperature=296.600 | | Etotal =543.428 grad(E)=63.898 E(BOND)=213.924 E(ANGL)=400.442 | | E(DIHE)=0.000 E(IMPR)=103.796 E(VDW )=-208.248 E(ELEC)=-128.054 | | E(CDIH)=22.273 E(NOE )=122.616 E(PLAN)=16.680 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 61869 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 61839 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 61846 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 61785 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 61880 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 61976 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62042 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=1159.670 E(kin)=597.909 temperature=296.289 | | Etotal =561.760 grad(E)=63.266 E(BOND)=219.205 E(ANGL)=409.015 | | E(DIHE)=0.000 E(IMPR)=91.334 E(VDW )=-214.872 E(ELEC)=-123.242 | | E(CDIH)=26.374 E(NOE )=139.339 E(PLAN)=14.608 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62059 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62151 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62174 intra-atom interactions NBONDS: found 62270 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart NBONDS: found 62411 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62410 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62484 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62477 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=1166.519 E(kin)=603.450 temperature=299.035 | | Etotal =563.069 grad(E)=63.236 E(BOND)=215.044 E(ANGL)=400.761 | | E(DIHE)=0.000 E(IMPR)=100.662 E(VDW )=-210.724 E(ELEC)=-132.889 | | E(CDIH)=32.390 E(NOE )=140.333 E(PLAN)=17.492 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1140.418 E(kin)=605.302 temperature=299.952 | | Etotal =535.116 grad(E)=64.425 E(BOND)=208.257 E(ANGL)=405.230 | | E(DIHE)=0.000 E(IMPR)=94.527 E(VDW )=-217.971 E(ELEC)=-130.330 | | E(CDIH)=22.116 E(NOE )=136.284 E(PLAN)=17.002 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=16.921 E(kin)=12.635 temperature=6.261 | | Etotal =20.802 grad(E)=1.407 E(BOND)=9.755 E(ANGL)=13.055 | | E(DIHE)=0.000 E(IMPR)=6.926 E(VDW )=8.584 E(ELEC)=5.343 | | E(CDIH)=5.106 E(NOE )=11.790 E(PLAN)=1.994 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=1144.916 E(kin)=604.339 temperature=299.475 | | Etotal =540.577 grad(E)=64.203 E(BOND)=208.866 E(ANGL)=401.865 | | E(DIHE)=0.000 E(IMPR)=93.829 E(VDW )=-213.460 E(ELEC)=-129.955 | | E(CDIH)=20.591 E(NOE )=141.622 E(PLAN)=17.217 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=35.089 E(kin)=18.186 temperature=9.012 | | Etotal =29.779 grad(E)=1.662 E(BOND)=11.575 E(ANGL)=15.579 | | E(DIHE)=0.000 E(IMPR)=7.260 E(VDW )=10.960 E(ELEC)=6.164 | | E(CDIH)=5.183 E(NOE )=13.749 E(PLAN)=2.243 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62530 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62603 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 62664 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62761 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62839 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 62784 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62747 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=1173.117 E(kin)=597.485 temperature=296.079 | | Etotal =575.633 grad(E)=65.991 E(BOND)=217.239 E(ANGL)=409.326 | | E(DIHE)=0.000 E(IMPR)=101.194 E(VDW )=-204.421 E(ELEC)=-136.693 | | E(CDIH)=26.932 E(NOE )=143.915 E(PLAN)=18.140 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62753 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.46 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62789 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62820 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62830 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62819 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 62682 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=1164.949 E(kin)=617.193 temperature=305.845 | | Etotal =547.756 grad(E)=65.296 E(BOND)=212.391 E(ANGL)=400.092 | | E(DIHE)=0.000 E(IMPR)=98.322 E(VDW )=-215.201 E(ELEC)=-123.662 | | E(CDIH)=13.260 E(NOE )=147.502 E(PLAN)=15.052 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62663 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 62595 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62597 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62594 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62601 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62608 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=1152.778 E(kin)=595.676 temperature=295.182 | | Etotal =557.102 grad(E)=66.073 E(BOND)=217.545 E(ANGL)=398.725 | | E(DIHE)=0.000 E(IMPR)=97.533 E(VDW )=-214.697 E(ELEC)=-125.905 | | E(CDIH)=22.900 E(NOE )=142.439 E(PLAN)=18.562 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart NBONDS: found 62540 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 62498 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62474 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62577 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62544 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=1151.311 E(kin)=596.746 temperature=295.713 | | Etotal =554.565 grad(E)=67.105 E(BOND)=225.267 E(ANGL)=400.873 | | E(DIHE)=0.000 E(IMPR)=106.134 E(VDW )=-203.021 E(ELEC)=-139.111 | | E(CDIH)=16.095 E(NOE )=131.299 E(PLAN)=17.029 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.30 A apart NBONDS: found 62553 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62579 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart NBONDS: found 62558 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62553 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62512 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62532 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart NBONDS: found 62606 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=1144.503 E(kin)=598.474 temperature=296.569 | | Etotal =546.029 grad(E)=65.737 E(BOND)=206.606 E(ANGL)=394.733 | | E(DIHE)=0.000 E(IMPR)=101.020 E(VDW )=-209.180 E(ELEC)=-146.577 | | E(CDIH)=21.279 E(NOE )=157.326 E(PLAN)=20.822 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62597 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62597 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 62614 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 62707 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart NBONDS: found 62758 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 62752 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62822 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=1147.920 E(kin)=623.941 temperature=309.189 | | Etotal =523.979 grad(E)=61.686 E(BOND)=210.483 E(ANGL)=400.400 | | E(DIHE)=0.000 E(IMPR)=98.358 E(VDW )=-232.477 E(ELEC)=-133.779 | | E(CDIH)=15.409 E(NOE )=152.494 E(PLAN)=13.092 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62877 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62929 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62976 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62975 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63059 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.22 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63177 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=1150.183 E(kin)=606.756 temperature=300.673 | | Etotal =543.427 grad(E)=66.161 E(BOND)=209.236 E(ANGL)=407.961 | | E(DIHE)=0.000 E(IMPR)=94.694 E(VDW )=-209.494 E(ELEC)=-137.451 | | E(CDIH)=23.617 E(NOE )=142.490 E(PLAN)=12.372 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63240 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " 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 63248 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63187 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63203 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63262 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=1149.375 E(kin)=603.265 temperature=298.943 | | Etotal =546.110 grad(E)=65.876 E(BOND)=214.264 E(ANGL)=409.396 | | E(DIHE)=0.000 E(IMPR)=105.879 E(VDW )=-202.002 E(ELEC)=-136.734 | | E(CDIH)=11.484 E(NOE )=128.454 E(PLAN)=15.370 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63278 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63279 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63331 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63394 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63435 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63497 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=1112.665 E(kin)=608.558 temperature=301.566 | | Etotal =504.107 grad(E)=66.066 E(BOND)=215.889 E(ANGL)=383.687 | | E(DIHE)=0.000 E(IMPR)=90.021 E(VDW )=-225.908 E(ELEC)=-138.179 | | E(CDIH)=28.827 E(NOE )=131.720 E(PLAN)=18.052 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63459 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 63450 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63455 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63425 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63409 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63395 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=1157.499 E(kin)=606.333 temperature=300.463 | | Etotal =551.166 grad(E)=65.166 E(BOND)=216.906 E(ANGL)=420.666 | | E(DIHE)=0.000 E(IMPR)=93.226 E(VDW )=-220.564 E(ELEC)=-132.078 | | E(CDIH)=21.507 E(NOE )=134.900 E(PLAN)=16.604 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1151.759 E(kin)=605.510 temperature=300.056 | | Etotal =546.249 grad(E)=65.507 E(BOND)=208.721 E(ANGL)=409.579 | | E(DIHE)=0.000 E(IMPR)=97.926 E(VDW )=-211.881 E(ELEC)=-133.547 | | E(CDIH)=20.799 E(NOE )=137.802 E(PLAN)=16.851 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=14.060 E(kin)=12.351 temperature=6.120 | | Etotal =18.339 grad(E)=1.369 E(BOND)=10.251 E(ANGL)=14.039 | | E(DIHE)=0.000 E(IMPR)=7.040 E(VDW )=10.095 E(ELEC)=6.129 | | E(CDIH)=5.259 E(NOE )=10.839 E(PLAN)=2.257 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=1147.197 E(kin)=604.729 temperature=299.669 | | Etotal =542.468 grad(E)=64.638 E(BOND)=208.817 E(ANGL)=404.436 | | E(DIHE)=0.000 E(IMPR)=95.195 E(VDW )=-212.933 E(ELEC)=-131.152 | | E(CDIH)=20.661 E(NOE )=140.349 E(PLAN)=17.095 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=29.952 E(kin)=16.482 temperature=8.167 | | Etotal =26.654 grad(E)=1.686 E(BOND)=11.151 E(ANGL)=15.515 | | E(DIHE)=0.000 E(IMPR)=7.443 E(VDW )=10.705 E(ELEC)=6.381 | | E(CDIH)=5.210 E(NOE )=12.978 E(PLAN)=2.254 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63380 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63378 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -11 -ADE -HO2'" only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63344 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63370 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63410 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63384 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63421 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63462 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=1147.626 E(kin)=622.761 temperature=308.604 | | Etotal =524.865 grad(E)=66.800 E(BOND)=214.562 E(ANGL)=400.364 | | E(DIHE)=0.000 E(IMPR)=95.914 E(VDW )=-223.634 E(ELEC)=-135.123 | | E(CDIH)=18.533 E(NOE )=136.519 E(PLAN)=17.730 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63487 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63518 intra-atom interactions %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63546 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63522 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63538 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 63473 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63421 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 63443 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63502 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=1140.377 E(kin)=605.697 temperature=300.148 | | Etotal =534.680 grad(E)=67.391 E(BOND)=221.985 E(ANGL)=403.318 | | E(DIHE)=0.000 E(IMPR)=92.771 E(VDW )=-221.761 E(ELEC)=-128.077 | | E(CDIH)=34.357 E(NOE )=115.349 E(PLAN)=16.738 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63450 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63460 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63448 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63421 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63447 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63426 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63420 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63432 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=1138.906 E(kin)=593.133 temperature=293.922 | | Etotal =545.773 grad(E)=66.077 E(BOND)=217.613 E(ANGL)=422.342 | | E(DIHE)=0.000 E(IMPR)=94.533 E(VDW )=-227.009 E(ELEC)=-130.498 | | E(CDIH)=22.910 E(NOE )=131.560 E(PLAN)=14.320 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63449 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63468 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63490 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63507 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63572 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63571 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63644 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63642 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63626 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 -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63592 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=1158.207 E(kin)=619.365 temperature=306.921 | | Etotal =538.842 grad(E)=66.894 E(BOND)=228.805 E(ANGL)=400.532 | | E(DIHE)=0.000 E(IMPR)=80.531 E(VDW )=-201.763 E(ELEC)=-122.951 | | E(CDIH)=13.955 E(NOE )=123.634 E(PLAN)=16.100 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63591 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63532 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63396 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63332 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63292 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63241 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63183 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63125 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63132 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63094 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=1123.409 E(kin)=600.499 temperature=297.572 | | Etotal =522.910 grad(E)=65.573 E(BOND)=202.728 E(ANGL)=403.261 | | E(DIHE)=0.000 E(IMPR)=107.929 E(VDW )=-232.217 E(ELEC)=-128.105 | | E(CDIH)=21.059 E(NOE )=134.887 E(PLAN)=13.368 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63089 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63012 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62904 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62810 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62666 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 62645 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62594 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62564 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62549 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=1150.332 E(kin)=618.288 temperature=306.387 | | Etotal =532.044 grad(E)=64.103 E(BOND)=201.020 E(ANGL)=405.511 | | E(DIHE)=0.000 E(IMPR)=97.535 E(VDW )=-213.860 E(ELEC)=-123.860 | | E(CDIH)=26.043 E(NOE )=120.072 E(PLAN)=19.584 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 62524 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 62570 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 62651 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 62698 intra-atom interactions %atoms "A -9 -URI -H5' " and "A -10 -CYT -HO2'" only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62672 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 62670 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62729 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 62697 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62708 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62744 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=1154.674 E(kin)=599.341 temperature=296.998 | | Etotal =555.334 grad(E)=66.558 E(BOND)=208.813 E(ANGL)=416.382 | | E(DIHE)=0.000 E(IMPR)=99.547 E(VDW )=-213.686 E(ELEC)=-131.755 | | E(CDIH)=16.962 E(NOE )=141.619 E(PLAN)=17.452 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62752 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62743 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62741 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62774 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 62859 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 62846 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62930 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63064 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=1144.223 E(kin)=611.682 temperature=303.114 | | Etotal =532.541 grad(E)=65.816 E(BOND)=198.749 E(ANGL)=405.950 | | E(DIHE)=0.000 E(IMPR)=98.453 E(VDW )=-217.167 E(ELEC)=-126.502 | | E(CDIH)=20.962 E(NOE )=133.169 E(PLAN)=18.927 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " 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 63220 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63250 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63300 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63355 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63360 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " 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 63395 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63389 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63304 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=1164.046 E(kin)=577.392 temperature=286.122 | | Etotal =586.654 grad(E)=66.477 E(BOND)=221.840 E(ANGL)=436.500 | | E(DIHE)=0.000 E(IMPR)=90.096 E(VDW )=-214.174 E(ELEC)=-117.071 | | E(CDIH)=17.413 E(NOE )=138.543 E(PLAN)=13.508 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63273 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63313 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " 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 NBONDS: found 63309 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63367 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63360 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63353 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 63343 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63334 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=1149.414 E(kin)=592.086 temperature=293.403 | | Etotal =557.329 grad(E)=64.877 E(BOND)=219.568 E(ANGL)=391.398 | | E(DIHE)=0.000 E(IMPR)=101.421 E(VDW )=-215.697 E(ELEC)=-138.748 | | E(CDIH)=19.159 E(NOE )=160.963 E(PLAN)=19.265 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1144.532 E(kin)=605.499 temperature=300.050 | | Etotal =539.033 grad(E)=65.842 E(BOND)=209.532 E(ANGL)=409.969 | | E(DIHE)=0.000 E(IMPR)=97.050 E(VDW )=-220.996 E(ELEC)=-127.932 | | E(CDIH)=21.237 E(NOE )=133.503 E(PLAN)=16.670 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.737 E(kin)=12.461 temperature=6.175 | | Etotal =16.004 grad(E)=1.375 E(BOND)=10.038 E(ANGL)=13.418 | | E(DIHE)=0.000 E(IMPR)=6.951 E(VDW )=9.018 E(ELEC)=6.585 | | E(CDIH)=5.062 E(NOE )=10.084 E(PLAN)=2.189 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=1146.531 E(kin)=604.922 temperature=299.764 | | Etotal =541.609 grad(E)=64.939 E(BOND)=208.996 E(ANGL)=405.819 | | E(DIHE)=0.000 E(IMPR)=95.659 E(VDW )=-214.949 E(ELEC)=-130.347 | | E(CDIH)=20.805 E(NOE )=138.637 E(PLAN)=16.989 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=26.514 E(kin)=15.578 temperature=7.719 | | Etotal =24.476 grad(E)=1.696 E(BOND)=10.888 E(ANGL)=15.208 | | E(DIHE)=0.000 E(IMPR)=7.367 E(VDW )=10.885 E(ELEC)=6.582 | | E(CDIH)=5.179 E(NOE )=12.670 E(PLAN)=2.246 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63213 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 63198 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63153 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 63143 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63127 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63079 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63109 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63133 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=1131.363 E(kin)=612.520 temperature=303.529 | | Etotal =518.843 grad(E)=66.690 E(BOND)=200.571 E(ANGL)=387.988 | | E(DIHE)=0.000 E(IMPR)=106.285 E(VDW )=-216.776 E(ELEC)=-132.085 | | E(CDIH)=28.206 E(NOE )=128.148 E(PLAN)=16.506 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63135 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63183 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63203 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63176 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart NBONDS: found 63300 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63436 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63465 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63490 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.28 A apart NBONDS: found 63548 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=1151.496 E(kin)=618.078 temperature=306.283 | | Etotal =533.419 grad(E)=66.575 E(BOND)=200.660 E(ANGL)=418.066 | | E(DIHE)=0.000 E(IMPR)=90.397 E(VDW )=-211.323 E(ELEC)=-131.900 | | E(CDIH)=12.531 E(NOE )=135.377 E(PLAN)=19.612 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63656 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63677 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63708 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " 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 63747 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63824 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " 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 63927 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64031 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " 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 64093 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=1164.046 E(kin)=606.740 temperature=300.665 | | Etotal =557.306 grad(E)=66.428 E(BOND)=213.459 E(ANGL)=408.987 | | E(DIHE)=0.000 E(IMPR)=104.404 E(VDW )=-215.769 E(ELEC)=-136.939 | | E(CDIH)=18.958 E(NOE )=145.207 E(PLAN)=19.000 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64143 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64133 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64086 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64106 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64077 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64099 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64101 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64094 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64094 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64058 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 64072 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=1135.452 E(kin)=612.575 temperature=303.557 | | Etotal =522.877 grad(E)=65.336 E(BOND)=209.419 E(ANGL)=398.216 | | E(DIHE)=0.000 E(IMPR)=99.392 E(VDW )=-207.503 E(ELEC)=-139.838 | | E(CDIH)=10.359 E(NOE )=134.748 E(PLAN)=18.084 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64107 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64160 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64222 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64220 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64202 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64194 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64162 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64196 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64137 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=1153.637 E(kin)=579.159 temperature=286.997 | | Etotal =574.478 grad(E)=70.161 E(BOND)=224.564 E(ANGL)=420.754 | | E(DIHE)=0.000 E(IMPR)=97.825 E(VDW )=-211.211 E(ELEC)=-133.605 | | E(CDIH)=10.128 E(NOE )=150.295 E(PLAN)=15.729 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64061 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64059 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63997 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64027 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64042 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63971 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 64006 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64033 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64003 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=1159.122 E(kin)=623.883 temperature=309.160 | | Etotal =535.239 grad(E)=63.190 E(BOND)=200.972 E(ANGL)=391.169 | | E(DIHE)=0.000 E(IMPR)=100.626 E(VDW )=-223.891 E(ELEC)=-130.597 | | E(CDIH)=18.527 E(NOE )=156.897 E(PLAN)=21.537 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 64051 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64145 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64202 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64187 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 64177 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 64192 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 64207 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64156 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64133 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=1142.962 E(kin)=602.019 temperature=298.326 | | Etotal =540.943 grad(E)=64.907 E(BOND)=205.566 E(ANGL)=410.926 | | E(DIHE)=0.000 E(IMPR)=86.563 E(VDW )=-208.225 E(ELEC)=-128.640 | | E(CDIH)=15.314 E(NOE )=142.390 E(PLAN)=17.048 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64160 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64051 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63963 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 63916 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63815 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63747 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63712 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63702 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63666 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=1155.913 E(kin)=609.383 temperature=301.975 | | Etotal =546.530 grad(E)=66.657 E(BOND)=204.545 E(ANGL)=424.851 | | E(DIHE)=0.000 E(IMPR)=90.825 E(VDW )=-200.635 E(ELEC)=-138.106 | | E(CDIH)=15.877 E(NOE )=131.820 E(PLAN)=17.352 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63676 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63612 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63507 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63498 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63413 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63429 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63411 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63387 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63325 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63307 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=1147.269 E(kin)=597.983 temperature=296.326 | | Etotal =549.286 grad(E)=67.244 E(BOND)=231.688 E(ANGL)=408.394 | | E(DIHE)=0.000 E(IMPR)=91.248 E(VDW )=-227.854 E(ELEC)=-138.154 | | E(CDIH)=14.335 E(NOE )=150.586 E(PLAN)=19.043 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63312 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63219 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 63237 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 63222 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart NBONDS: found 63175 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63184 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63176 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63182 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63179 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63184 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=1142.287 E(kin)=586.422 temperature=290.597 | | Etotal =555.865 grad(E)=68.358 E(BOND)=220.979 E(ANGL)=422.791 | | E(DIHE)=0.000 E(IMPR)=104.509 E(VDW )=-204.357 E(ELEC)=-140.168 | | E(CDIH)=10.663 E(NOE )=125.103 E(PLAN)=16.346 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1149.414 E(kin)=605.505 temperature=300.053 | | Etotal =543.909 grad(E)=66.563 E(BOND)=214.521 E(ANGL)=406.929 | | E(DIHE)=0.000 E(IMPR)=96.764 E(VDW )=-213.559 E(ELEC)=-134.781 | | E(CDIH)=15.977 E(NOE )=141.328 E(PLAN)=16.731 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.647 E(kin)=12.105 temperature=5.999 | | Etotal =15.652 grad(E)=1.358 E(BOND)=9.646 E(ANGL)=13.485 | | E(DIHE)=0.000 E(IMPR)=6.471 E(VDW )=9.308 E(ELEC)=3.991 | | E(CDIH)=4.456 E(NOE )=11.153 E(PLAN)=1.999 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=1147.107 E(kin)=605.039 temperature=299.822 | | Etotal =542.069 grad(E)=65.264 E(BOND)=210.101 E(ANGL)=406.041 | | E(DIHE)=0.000 E(IMPR)=95.880 E(VDW )=-214.671 E(ELEC)=-131.234 | | E(CDIH)=19.839 E(NOE )=139.176 E(PLAN)=16.937 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=24.216 E(kin)=14.950 temperature=7.408 | | Etotal =23.002 grad(E)=1.759 E(BOND)=10.878 E(ANGL)=14.886 | | E(DIHE)=0.000 E(IMPR)=7.210 E(VDW )=10.603 E(ELEC)=6.402 | | E(CDIH)=5.400 E(NOE )=12.428 E(PLAN)=2.201 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63212 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63213 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63215 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63246 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63248 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " 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 63254 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " 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 63270 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63268 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63298 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=1151.868 E(kin)=617.746 temperature=306.119 | | Etotal =534.122 grad(E)=65.997 E(BOND)=229.347 E(ANGL)=408.121 | | E(DIHE)=0.000 E(IMPR)=87.899 E(VDW )=-223.754 E(ELEC)=-138.356 | | E(CDIH)=19.469 E(NOE )=133.081 E(PLAN)=18.314 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63367 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63317 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63287 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63254 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63187 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63175 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63185 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63205 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63168 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63169 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=1148.255 E(kin)=621.167 temperature=307.814 | | Etotal =527.088 grad(E)=66.806 E(BOND)=206.616 E(ANGL)=394.859 | | E(DIHE)=0.000 E(IMPR)=90.845 E(VDW )=-213.023 E(ELEC)=-126.207 | | E(CDIH)=26.083 E(NOE )=130.547 E(PLAN)=17.369 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63143 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63162 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63184 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63234 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63259 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63347 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63424 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63474 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 63477 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63497 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=1146.839 E(kin)=614.380 temperature=304.451 | | Etotal =532.458 grad(E)=64.944 E(BOND)=212.450 E(ANGL)=385.031 | | E(DIHE)=0.000 E(IMPR)=95.193 E(VDW )=-201.053 E(ELEC)=-144.181 | | E(CDIH)=18.858 E(NOE )=146.104 E(PLAN)=20.057 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63481 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63474 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63499 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63482 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63529 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63532 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63519 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63522 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=1148.073 E(kin)=614.497 temperature=304.509 | | Etotal =533.576 grad(E)=66.726 E(BOND)=209.903 E(ANGL)=422.121 | | E(DIHE)=0.000 E(IMPR)=102.423 E(VDW )=-222.814 E(ELEC)=-135.576 | | E(CDIH)=19.389 E(NOE )=124.486 E(PLAN)=13.644 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63532 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63535 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63539 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63564 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63544 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63549 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63534 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63446 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63415 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63411 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63356 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=1156.455 E(kin)=615.304 temperature=304.909 | | Etotal =541.152 grad(E)=68.036 E(BOND)=230.349 E(ANGL)=403.877 | | E(DIHE)=0.000 E(IMPR)=94.606 E(VDW )=-218.607 E(ELEC)=-125.336 | | E(CDIH)=14.417 E(NOE )=125.893 E(PLAN)=15.952 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63241 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63243 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63199 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63152 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63074 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63002 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62961 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62930 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62935 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62908 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 62881 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=1162.214 E(kin)=619.157 temperature=306.818 | | Etotal =543.057 grad(E)=67.436 E(BOND)=223.465 E(ANGL)=400.758 | | E(DIHE)=0.000 E(IMPR)=94.516 E(VDW )=-218.565 E(ELEC)=-132.530 | | E(CDIH)=22.652 E(NOE )=136.546 E(PLAN)=16.216 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62902 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62885 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62865 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62794 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62701 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62672 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 62713 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 62734 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 62749 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=1161.736 E(kin)=604.235 temperature=299.424 | | Etotal =557.501 grad(E)=67.196 E(BOND)=233.001 E(ANGL)=403.244 | | E(DIHE)=0.000 E(IMPR)=86.709 E(VDW )=-219.296 E(ELEC)=-129.158 | | E(CDIH)=34.121 E(NOE )=130.263 E(PLAN)=18.617 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62821 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 62840 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62834 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62850 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62847 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62879 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62906 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62927 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62943 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63007 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63088 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=1130.583 E(kin)=593.528 temperature=294.118 | | Etotal =537.055 grad(E)=67.391 E(BOND)=218.237 E(ANGL)=408.198 | | E(DIHE)=0.000 E(IMPR)=100.500 E(VDW )=-226.001 E(ELEC)=-129.554 | | E(CDIH)=25.829 E(NOE )=125.781 E(PLAN)=14.065 | ------------------------------------------------------------------------------- %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63149 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63166 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63220 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63207 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63232 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63254 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63274 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 63221 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 63198 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63179 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63166 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63147 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=1140.355 E(kin)=602.442 temperature=298.535 | | Etotal =537.913 grad(E)=66.904 E(BOND)=202.166 E(ANGL)=418.184 | | E(DIHE)=0.000 E(IMPR)=100.368 E(VDW )=-223.347 E(ELEC)=-135.024 | | E(CDIH)=20.362 E(NOE )=136.639 E(PLAN)=18.565 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63187 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63166 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63153 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63080 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.13 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.41 A apart NBONDS: found 63061 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.40 A apart NBONDS: found 63034 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 63000 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 62935 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 62926 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62955 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62943 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=1148.788 E(kin)=602.752 temperature=298.689 | | Etotal =546.035 grad(E)=69.746 E(BOND)=228.584 E(ANGL)=413.015 | | E(DIHE)=0.000 E(IMPR)=101.659 E(VDW )=-228.389 E(ELEC)=-138.135 | | E(CDIH)=16.438 E(NOE )=134.397 E(PLAN)=18.467 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1144.010 E(kin)=605.456 temperature=300.029 | | Etotal =538.554 grad(E)=67.087 E(BOND)=213.375 E(ANGL)=411.901 | | E(DIHE)=0.000 E(IMPR)=98.416 E(VDW )=-220.355 E(ELEC)=-133.429 | | E(CDIH)=20.074 E(NOE )=132.461 E(PLAN)=16.110 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.125 E(kin)=12.361 temperature=6.125 | | Etotal =15.553 grad(E)=1.378 E(BOND)=10.507 E(ANGL)=12.629 | | E(DIHE)=0.000 E(IMPR)=6.399 E(VDW )=7.989 E(ELEC)=6.280 | | E(CDIH)=4.954 E(NOE )=9.747 E(PLAN)=1.917 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=1146.591 E(kin)=605.108 temperature=299.856 | | Etotal =541.483 grad(E)=65.568 E(BOND)=210.647 E(ANGL)=407.018 | | E(DIHE)=0.000 E(IMPR)=96.302 E(VDW )=-215.618 E(ELEC)=-131.600 | | E(CDIH)=19.878 E(NOE )=138.056 E(PLAN)=16.799 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=22.519 E(kin)=14.551 temperature=7.211 | | Etotal =21.976 grad(E)=1.832 E(BOND)=10.886 E(ANGL)=14.697 | | E(DIHE)=0.000 E(IMPR)=7.144 E(VDW )=10.431 E(ELEC)=6.434 | | E(CDIH)=5.329 E(NOE )=12.281 E(PLAN)=2.178 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62960 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " 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 63012 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63003 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63061 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63042 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63038 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62966 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62927 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62822 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 62783 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=1142.490 E(kin)=604.295 temperature=299.454 | | Etotal =538.195 grad(E)=65.782 E(BOND)=208.870 E(ANGL)=417.138 | | E(DIHE)=0.000 E(IMPR)=95.875 E(VDW )=-222.711 E(ELEC)=-133.936 | | E(CDIH)=27.664 E(NOE )=128.474 E(PLAN)=16.820 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 62653 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62653 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62672 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 62674 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62655 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62706 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 62750 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62756 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62759 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=1145.361 E(kin)=627.829 temperature=311.115 | | Etotal =517.533 grad(E)=65.978 E(BOND)=195.679 E(ANGL)=404.898 | | E(DIHE)=0.000 E(IMPR)=101.826 E(VDW )=-221.738 E(ELEC)=-137.524 | | E(CDIH)=22.664 E(NOE )=136.156 E(PLAN)=15.572 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62783 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 62877 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 62941 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62988 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63100 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63232 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63329 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63412 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.47 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63499 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63520 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=1137.112 E(kin)=613.987 temperature=304.256 | | Etotal =523.125 grad(E)=65.673 E(BOND)=213.748 E(ANGL)=408.859 | | E(DIHE)=0.000 E(IMPR)=94.082 E(VDW )=-217.737 E(ELEC)=-141.177 | | E(CDIH)=22.303 E(NOE )=125.722 E(PLAN)=17.326 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63439 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63385 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63317 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63249 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63193 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63208 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=1147.804 E(kin)=600.137 temperature=297.393 | | Etotal =547.667 grad(E)=67.140 E(BOND)=218.181 E(ANGL)=410.924 | | E(DIHE)=0.000 E(IMPR)=102.594 E(VDW )=-221.279 E(ELEC)=-134.452 | | E(CDIH)=9.034 E(NOE )=145.803 E(PLAN)=16.862 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63242 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 -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63256 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63298 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63312 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63354 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63370 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63397 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63379 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=1147.443 E(kin)=632.181 temperature=313.272 | | Etotal =515.262 grad(E)=67.034 E(BOND)=209.335 E(ANGL)=412.414 | | E(DIHE)=0.000 E(IMPR)=94.516 E(VDW )=-225.132 E(ELEC)=-146.639 | | E(CDIH)=24.994 E(NOE )=128.635 E(PLAN)=17.139 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63206 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63126 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63034 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62944 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62914 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62843 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62854 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " 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 62841 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62825 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=1137.472 E(kin)=607.868 temperature=301.224 | | Etotal =529.604 grad(E)=66.237 E(BOND)=219.991 E(ANGL)=404.404 | | E(DIHE)=0.000 E(IMPR)=98.089 E(VDW )=-207.711 E(ELEC)=-145.006 | | E(CDIH)=26.674 E(NOE )=114.975 E(PLAN)=18.189 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62834 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62789 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 62767 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62790 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62748 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62682 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62709 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62718 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=1172.178 E(kin)=604.586 temperature=299.598 | | Etotal =567.592 grad(E)=69.978 E(BOND)=231.718 E(ANGL)=424.610 | | E(DIHE)=0.000 E(IMPR)=93.173 E(VDW )=-228.221 E(ELEC)=-128.628 | | E(CDIH)=13.712 E(NOE )=143.099 E(PLAN)=18.129 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " 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 62709 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62748 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62761 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62843 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62870 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62865 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62851 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62833 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62795 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=1145.674 E(kin)=614.282 temperature=304.403 | | Etotal =531.392 grad(E)=67.362 E(BOND)=207.698 E(ANGL)=397.981 | | E(DIHE)=0.000 E(IMPR)=90.469 E(VDW )=-214.977 E(ELEC)=-148.543 | | E(CDIH)=21.879 E(NOE )=161.560 E(PLAN)=15.326 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62734 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62727 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62795 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 -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " 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 62832 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 -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62825 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62918 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 62979 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.30 A apart NBONDS: found 62956 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62938 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=1140.856 E(kin)=611.886 temperature=303.215 | | Etotal =528.970 grad(E)=67.239 E(BOND)=218.994 E(ANGL)=413.130 | | E(DIHE)=0.000 E(IMPR)=98.243 E(VDW )=-210.984 E(ELEC)=-140.678 | | E(CDIH)=14.593 E(NOE )=117.538 E(PLAN)=18.134 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " 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 62924 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " 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 62926 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 -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " 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 62922 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62904 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62927 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62976 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63063 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63148 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63152 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=1164.715 E(kin)=600.456 temperature=297.551 | | Etotal =564.259 grad(E)=68.472 E(BOND)=228.729 E(ANGL)=415.651 | | E(DIHE)=0.000 E(IMPR)=88.709 E(VDW )=-200.776 E(ELEC)=-144.067 | | E(CDIH)=23.678 E(NOE )=134.800 E(PLAN)=17.536 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1148.875 E(kin)=605.418 temperature=300.010 | | Etotal =543.457 grad(E)=67.225 E(BOND)=220.766 E(ANGL)=411.335 | | E(DIHE)=0.000 E(IMPR)=95.935 E(VDW )=-217.611 E(ELEC)=-138.683 | | E(CDIH)=19.712 E(NOE )=135.409 E(PLAN)=16.594 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.044 E(kin)=12.529 temperature=6.209 | | Etotal =16.329 grad(E)=1.399 E(BOND)=10.594 E(ANGL)=12.556 | | E(DIHE)=0.000 E(IMPR)=6.799 E(VDW )=8.400 E(ELEC)=6.145 | | E(CDIH)=4.705 E(NOE )=10.516 E(PLAN)=1.870 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=1146.918 E(kin)=605.152 temperature=299.878 | | Etotal =541.765 grad(E)=65.804 E(BOND)=212.092 E(ANGL)=407.635 | | E(DIHE)=0.000 E(IMPR)=96.250 E(VDW )=-215.903 E(ELEC)=-132.612 | | E(CDIH)=19.855 E(NOE )=137.678 E(PLAN)=16.770 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=21.277 E(kin)=14.280 temperature=7.076 | | Etotal =21.273 grad(E)=1.869 E(BOND)=11.408 E(ANGL)=14.490 | | E(DIHE)=0.000 E(IMPR)=7.097 E(VDW )=10.190 E(ELEC)=6.858 | | E(CDIH)=5.245 E(NOE )=12.080 E(PLAN)=2.138 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63168 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63119 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63127 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " 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 63170 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63169 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63216 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63287 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=1145.403 E(kin)=611.727 temperature=303.137 | | Etotal =533.675 grad(E)=65.754 E(BOND)=200.231 E(ANGL)=421.189 | | E(DIHE)=0.000 E(IMPR)=95.068 E(VDW )=-229.841 E(ELEC)=-137.838 | | E(CDIH)=18.836 E(NOE )=150.089 E(PLAN)=15.941 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 63331 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 63459 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63403 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 63341 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63202 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63201 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 -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63115 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63111 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=1139.677 E(kin)=580.586 temperature=287.705 | | Etotal =559.091 grad(E)=68.549 E(BOND)=220.401 E(ANGL)=411.753 | | E(DIHE)=0.000 E(IMPR)=106.594 E(VDW )=-228.445 E(ELEC)=-137.064 | | E(CDIH)=24.726 E(NOE )=144.662 E(PLAN)=16.464 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63186 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 -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63221 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63261 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63300 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63305 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63281 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 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 1.45 A apart NBONDS: found 63291 intra-atom interactions %atoms "A -9 -URI -H5' " and "A -10 -CYT -HO2'" only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63312 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=1146.347 E(kin)=611.760 temperature=303.153 | | Etotal =534.587 grad(E)=66.855 E(BOND)=220.178 E(ANGL)=412.625 | | E(DIHE)=0.000 E(IMPR)=89.001 E(VDW )=-208.946 E(ELEC)=-136.715 | | E(CDIH)=17.114 E(NOE )=123.976 E(PLAN)=17.354 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63309 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63285 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63256 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63215 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 -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63219 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63184 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63178 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63152 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=1139.578 E(kin)=594.953 temperature=294.824 | | Etotal =544.625 grad(E)=68.316 E(BOND)=231.022 E(ANGL)=407.730 | | E(DIHE)=0.000 E(IMPR)=101.214 E(VDW )=-223.763 E(ELEC)=-134.297 | | E(CDIH)=15.577 E(NOE )=129.722 E(PLAN)=17.419 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63180 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63191 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63173 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63136 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart NBONDS: found 63087 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63047 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62978 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 62917 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=1124.487 E(kin)=595.861 temperature=295.274 | | Etotal =528.626 grad(E)=68.259 E(BOND)=210.439 E(ANGL)=416.341 | | E(DIHE)=0.000 E(IMPR)=86.845 E(VDW )=-221.641 E(ELEC)=-135.467 | | E(CDIH)=14.617 E(NOE )=142.805 E(PLAN)=14.686 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 62797 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 62776 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 62777 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 62745 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62842 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62853 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 -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62882 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=1174.968 E(kin)=629.079 temperature=311.735 | | Etotal =545.889 grad(E)=65.707 E(BOND)=207.638 E(ANGL)=420.236 | | E(DIHE)=0.000 E(IMPR)=92.336 E(VDW )=-206.534 E(ELEC)=-134.148 | | E(CDIH)=20.607 E(NOE )=129.058 E(PLAN)=16.696 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " 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 62967 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62982 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62977 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63042 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63072 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63037 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=1142.469 E(kin)=601.518 temperature=298.077 | | Etotal =540.951 grad(E)=69.257 E(BOND)=225.798 E(ANGL)=411.344 | | E(DIHE)=0.000 E(IMPR)=110.486 E(VDW )=-236.921 E(ELEC)=-140.491 | | E(CDIH)=18.531 E(NOE )=137.564 E(PLAN)=14.640 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63124 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63088 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63100 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63096 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63119 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63223 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=1154.566 E(kin)=614.447 temperature=304.484 | | Etotal =540.119 grad(E)=67.821 E(BOND)=219.036 E(ANGL)=420.631 | | E(DIHE)=0.000 E(IMPR)=89.240 E(VDW )=-220.701 E(ELEC)=-143.973 | | E(CDIH)=26.378 E(NOE )=133.292 E(PLAN)=16.215 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63264 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63348 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63413 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " 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 63272 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63208 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63200 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=1146.526 E(kin)=595.494 temperature=295.092 | | Etotal =551.032 grad(E)=68.703 E(BOND)=218.138 E(ANGL)=429.051 | | E(DIHE)=0.000 E(IMPR)=91.069 E(VDW )=-213.404 E(ELEC)=-137.567 | | E(CDIH)=16.987 E(NOE )=131.826 E(PLAN)=14.931 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63131 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63136 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.29 A apart NBONDS: found 63048 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 62986 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62892 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62859 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=1142.444 E(kin)=621.671 temperature=308.064 | | Etotal =520.773 grad(E)=66.973 E(BOND)=215.324 E(ANGL)=401.805 | | E(DIHE)=0.000 E(IMPR)=96.590 E(VDW )=-224.987 E(ELEC)=-133.148 | | E(CDIH)=27.042 E(NOE )=120.944 E(PLAN)=17.203 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1146.849 E(kin)=605.584 temperature=300.092 | | Etotal =541.265 grad(E)=67.288 E(BOND)=219.898 E(ANGL)=411.164 | | E(DIHE)=0.000 E(IMPR)=97.774 E(VDW )=-219.201 E(ELEC)=-137.748 | | E(CDIH)=19.988 E(NOE )=133.369 E(PLAN)=16.022 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.960 E(kin)=12.594 temperature=6.241 | | Etotal =16.975 grad(E)=1.426 E(BOND)=11.413 E(ANGL)=13.484 | | E(DIHE)=0.000 E(IMPR)=6.994 E(VDW )=7.799 E(ELEC)=3.709 | | E(CDIH)=4.277 E(NOE )=11.017 E(PLAN)=1.589 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=1146.909 E(kin)=605.206 temperature=299.905 | | Etotal =541.703 grad(E)=65.990 E(BOND)=213.068 E(ANGL)=408.076 | | E(DIHE)=0.000 E(IMPR)=96.440 E(VDW )=-216.315 E(ELEC)=-133.254 | | E(CDIH)=19.871 E(NOE )=137.140 E(PLAN)=16.677 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=20.347 E(kin)=14.081 temperature=6.978 | | Etotal =20.785 grad(E)=1.884 E(BOND)=11.697 E(ANGL)=14.415 | | E(DIHE)=0.000 E(IMPR)=7.102 E(VDW )=9.982 E(ELEC)=6.764 | | E(CDIH)=5.134 E(NOE )=12.037 E(PLAN)=2.092 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 62871 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62869 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62804 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62833 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62816 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=1153.767 E(kin)=606.334 temperature=300.464 | | Etotal =547.433 grad(E)=67.656 E(BOND)=240.620 E(ANGL)=391.392 | | E(DIHE)=0.000 E(IMPR)=91.398 E(VDW )=-206.634 E(ELEC)=-124.340 | | E(CDIH)=16.767 E(NOE )=124.212 E(PLAN)=14.017 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62807 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62803 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62742 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 62749 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62711 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62687 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=1160.864 E(kin)=610.614 temperature=302.585 | | Etotal =550.250 grad(E)=67.566 E(BOND)=211.750 E(ANGL)=439.528 | | E(DIHE)=0.000 E(IMPR)=84.074 E(VDW )=-217.074 E(ELEC)=-129.921 | | E(CDIH)=17.601 E(NOE )=128.454 E(PLAN)=15.838 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " 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 62710 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62716 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62707 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62785 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62856 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62840 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=1140.330 E(kin)=618.085 temperature=306.287 | | Etotal =522.245 grad(E)=65.944 E(BOND)=207.463 E(ANGL)=424.986 | | E(DIHE)=0.000 E(IMPR)=94.990 E(VDW )=-223.310 E(ELEC)=-135.553 | | E(CDIH)=19.918 E(NOE )=118.480 E(PLAN)=15.271 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62850 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart NBONDS: found 62864 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62852 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62855 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62824 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62879 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62897 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=1148.063 E(kin)=592.686 temperature=293.701 | | Etotal =555.377 grad(E)=68.958 E(BOND)=227.424 E(ANGL)=392.519 | | E(DIHE)=0.000 E(IMPR)=112.559 E(VDW )=-217.470 E(ELEC)=-140.097 | | E(CDIH)=22.067 E(NOE )=140.291 E(PLAN)=18.084 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62940 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 -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62955 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62916 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62863 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 62865 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.40 A apart NBONDS: found 62851 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62896 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=1158.620 E(kin)=603.345 temperature=298.983 | | Etotal =555.275 grad(E)=69.347 E(BOND)=215.689 E(ANGL)=421.174 | | E(DIHE)=0.000 E(IMPR)=99.267 E(VDW )=-217.845 E(ELEC)=-131.522 | | E(CDIH)=19.425 E(NOE )=133.718 E(PLAN)=15.368 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart NBONDS: found 62878 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63002 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63027 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63054 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63155 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63152 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=1142.761 E(kin)=608.002 temperature=301.291 | | Etotal =534.759 grad(E)=68.119 E(BOND)=209.013 E(ANGL)=411.101 | | E(DIHE)=0.000 E(IMPR)=102.653 E(VDW )=-219.451 E(ELEC)=-138.555 | | E(CDIH)=15.001 E(NOE )=137.310 E(PLAN)=17.687 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63191 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63271 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " 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 63381 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63484 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart NBONDS: found 63524 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=1149.546 E(kin)=618.097 temperature=306.293 | | Etotal =531.449 grad(E)=67.004 E(BOND)=217.437 E(ANGL)=402.596 | | E(DIHE)=0.000 E(IMPR)=101.145 E(VDW )=-217.861 E(ELEC)=-134.688 | | E(CDIH)=17.684 E(NOE )=128.181 E(PLAN)=16.956 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63671 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 -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63673 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63740 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63735 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63740 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63721 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63651 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=1147.328 E(kin)=594.618 temperature=294.658 | | Etotal =552.710 grad(E)=67.995 E(BOND)=228.005 E(ANGL)=417.495 | | E(DIHE)=0.000 E(IMPR)=103.126 E(VDW )=-222.342 E(ELEC)=-137.172 | | E(CDIH)=19.565 E(NOE )=128.821 E(PLAN)=15.213 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63612 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63596 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63621 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63598 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63602 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 63609 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 63672 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=1139.731 E(kin)=601.187 temperature=297.913 | | Etotal =538.544 grad(E)=68.245 E(BOND)=228.074 E(ANGL)=399.869 | | E(DIHE)=0.000 E(IMPR)=94.521 E(VDW )=-214.376 E(ELEC)=-138.014 | | E(CDIH)=20.285 E(NOE )=131.019 E(PLAN)=17.166 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.42 A apart NBONDS: found 63678 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63681 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart NBONDS: found 63684 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63722 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63778 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63840 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63894 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=1138.131 E(kin)=611.788 temperature=303.167 | | Etotal =526.342 grad(E)=66.184 E(BOND)=206.974 E(ANGL)=416.172 | | E(DIHE)=0.000 E(IMPR)=89.092 E(VDW )=-214.775 E(ELEC)=-139.319 | | E(CDIH)=16.436 E(NOE )=132.967 E(PLAN)=18.796 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1147.726 E(kin)=605.495 temperature=300.048 | | Etotal =542.232 grad(E)=68.201 E(BOND)=219.297 E(ANGL)=410.394 | | E(DIHE)=0.000 E(IMPR)=97.251 E(VDW )=-217.134 E(ELEC)=-135.318 | | E(CDIH)=18.268 E(NOE )=132.993 E(PLAN)=16.481 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.750 E(kin)=12.333 temperature=6.112 | | Etotal =14.159 grad(E)=1.482 E(BOND)=9.972 E(ANGL)=13.145 | | E(DIHE)=0.000 E(IMPR)=7.427 E(VDW )=9.334 E(ELEC)=4.808 | | E(CDIH)=4.753 E(NOE )=9.832 E(PLAN)=1.969 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=1147.000 E(kin)=605.238 temperature=299.921 | | Etotal =541.761 grad(E)=66.235 E(BOND)=213.760 E(ANGL)=408.333 | | E(DIHE)=0.000 E(IMPR)=96.530 E(VDW )=-216.406 E(ELEC)=-133.483 | | E(CDIH)=19.693 E(NOE )=136.679 E(PLAN)=16.655 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=19.358 E(kin)=13.898 temperature=6.887 | | Etotal =20.157 grad(E)=1.970 E(BOND)=11.683 E(ANGL)=14.298 | | E(DIHE)=0.000 E(IMPR)=7.144 E(VDW )=9.916 E(ELEC)=6.607 | | E(CDIH)=5.118 E(NOE )=11.884 E(PLAN)=2.080 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63925 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63834 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63819 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63726 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63728 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63789 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63781 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=1156.121 E(kin)=590.246 temperature=292.491 | | Etotal =565.875 grad(E)=68.475 E(BOND)=228.928 E(ANGL)=401.730 | | E(DIHE)=0.000 E(IMPR)=102.607 E(VDW )=-212.402 E(ELEC)=-127.723 | | E(CDIH)=13.708 E(NOE )=141.783 E(PLAN)=17.244 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63776 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63834 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63825 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63794 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63776 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63813 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " 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 NBONDS: found 63779 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " 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 NBONDS: found 63759 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63798 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=1153.251 E(kin)=627.646 temperature=311.025 | | Etotal =525.605 grad(E)=67.032 E(BOND)=207.555 E(ANGL)=406.438 | | E(DIHE)=0.000 E(IMPR)=93.855 E(VDW )=-215.468 E(ELEC)=-130.602 | | E(CDIH)=12.943 E(NOE )=136.488 E(PLAN)=14.395 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63842 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63808 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63831 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63785 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63781 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63781 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63779 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63760 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63760 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63706 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63714 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=1154.847 E(kin)=615.367 temperature=304.940 | | Etotal =539.481 grad(E)=68.908 E(BOND)=222.111 E(ANGL)=392.846 | | E(DIHE)=0.000 E(IMPR)=91.204 E(VDW )=-209.209 E(ELEC)=-125.151 | | E(CDIH)=12.984 E(NOE )=143.740 E(PLAN)=10.956 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63711 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63765 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63745 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63744 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63782 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 63756 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63711 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63625 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63559 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=1157.002 E(kin)=616.738 temperature=305.620 | | Etotal =540.264 grad(E)=69.988 E(BOND)=211.158 E(ANGL)=407.161 | | E(DIHE)=0.000 E(IMPR)=90.811 E(VDW )=-227.699 E(ELEC)=-140.422 | | E(CDIH)=17.039 E(NOE )=162.863 E(PLAN)=19.352 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63427 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63401 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63374 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63406 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63324 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " 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 63292 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63350 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63335 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63296 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63361 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=1163.665 E(kin)=589.320 temperature=292.033 | | Etotal =574.345 grad(E)=69.592 E(BOND)=233.426 E(ANGL)=401.915 | | E(DIHE)=0.000 E(IMPR)=101.182 E(VDW )=-204.064 E(ELEC)=-137.657 | | E(CDIH)=21.591 E(NOE )=137.627 E(PLAN)=20.326 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63396 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63389 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63381 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63465 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63495 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63478 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63566 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63549 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63541 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=1162.011 E(kin)=603.516 temperature=299.068 | | Etotal =558.495 grad(E)=69.981 E(BOND)=228.610 E(ANGL)=412.104 | | E(DIHE)=0.000 E(IMPR)=94.032 E(VDW )=-220.892 E(ELEC)=-129.917 | | E(CDIH)=16.451 E(NOE )=142.292 E(PLAN)=15.815 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63580 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63605 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63724 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63767 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63678 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63597 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=1130.748 E(kin)=586.979 temperature=290.873 | | Etotal =543.769 grad(E)=66.079 E(BOND)=216.610 E(ANGL)=427.194 | | E(DIHE)=0.000 E(IMPR)=88.918 E(VDW )=-220.776 E(ELEC)=-135.610 | | E(CDIH)=21.319 E(NOE )=127.637 E(PLAN)=18.477 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63545 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63425 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63395 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63310 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63245 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63291 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63307 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63417 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63459 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=1145.402 E(kin)=608.336 temperature=301.456 | | Etotal =537.066 grad(E)=69.766 E(BOND)=234.713 E(ANGL)=410.031 | | E(DIHE)=0.000 E(IMPR)=100.149 E(VDW )=-237.887 E(ELEC)=-134.816 | | E(CDIH)=9.917 E(NOE )=139.258 E(PLAN)=15.700 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63522 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63665 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63738 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63801 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63855 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63812 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63744 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=1149.351 E(kin)=611.617 temperature=303.082 | | Etotal =537.734 grad(E)=67.815 E(BOND)=222.555 E(ANGL)=394.513 | | E(DIHE)=0.000 E(IMPR)=96.640 E(VDW )=-212.653 E(ELEC)=-134.358 | | E(CDIH)=12.608 E(NOE )=141.496 E(PLAN)=16.933 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63677 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63629 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63584 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63615 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63626 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63577 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63619 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63639 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=1174.145 E(kin)=595.840 temperature=295.264 | | Etotal =578.305 grad(E)=70.935 E(BOND)=228.148 E(ANGL)=444.495 | | E(DIHE)=0.000 E(IMPR)=97.195 E(VDW )=-224.817 E(ELEC)=-139.753 | | E(CDIH)=20.103 E(NOE )=135.489 E(PLAN)=17.445 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1153.749 E(kin)=605.338 temperature=299.970 | | Etotal =548.411 grad(E)=68.653 E(BOND)=225.513 E(ANGL)=407.908 | | E(DIHE)=0.000 E(IMPR)=96.841 E(VDW )=-218.749 E(ELEC)=-133.377 | | E(CDIH)=16.782 E(NOE )=136.967 E(PLAN)=16.526 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.393 E(kin)=12.401 temperature=6.145 | | Etotal =14.563 grad(E)=1.498 E(BOND)=10.149 E(ANGL)=12.669 | | E(DIHE)=0.000 E(IMPR)=7.254 E(VDW )=6.572 E(ELEC)=4.066 | | E(CDIH)=4.500 E(NOE )=9.557 E(PLAN)=2.508 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=1147.675 E(kin)=605.248 temperature=299.926 | | Etotal =542.426 grad(E)=66.477 E(BOND)=214.935 E(ANGL)=408.291 | | E(DIHE)=0.000 E(IMPR)=96.561 E(VDW )=-216.640 E(ELEC)=-133.473 | | E(CDIH)=19.402 E(NOE )=136.708 E(PLAN)=16.642 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=18.666 E(kin)=13.756 temperature=6.817 | | Etotal =19.770 grad(E)=2.060 E(BOND)=12.066 E(ANGL)=14.145 | | E(DIHE)=0.000 E(IMPR)=7.155 E(VDW )=9.659 E(ELEC)=6.399 | | E(CDIH)=5.134 E(NOE )=11.672 E(PLAN)=2.127 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63668 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63660 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63619 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63585 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63551 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63588 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=1160.678 E(kin)=627.662 temperature=311.033 | | Etotal =533.016 grad(E)=67.278 E(BOND)=224.232 E(ANGL)=391.460 | | E(DIHE)=0.000 E(IMPR)=96.091 E(VDW )=-213.822 E(ELEC)=-134.787 | | E(CDIH)=18.180 E(NOE )=132.595 E(PLAN)=19.067 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63652 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63574 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63510 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63448 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63417 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63362 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=1153.436 E(kin)=590.711 temperature=292.722 | | Etotal =562.724 grad(E)=70.351 E(BOND)=247.575 E(ANGL)=410.080 | | E(DIHE)=0.000 E(IMPR)=97.952 E(VDW )=-216.118 E(ELEC)=-132.427 | | E(CDIH)=21.622 E(NOE )=117.478 E(PLAN)=16.562 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63292 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 -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63269 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63172 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63146 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=1151.016 E(kin)=622.264 temperature=308.358 | | Etotal =528.751 grad(E)=68.119 E(BOND)=208.581 E(ANGL)=414.353 | | E(DIHE)=0.000 E(IMPR)=90.131 E(VDW )=-222.831 E(ELEC)=-130.151 | | E(CDIH)=16.065 E(NOE )=138.305 E(PLAN)=14.300 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63201 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63157 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63203 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63249 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.31 A apart NBONDS: found 63272 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=1158.855 E(kin)=622.902 temperature=308.674 | | Etotal =535.953 grad(E)=66.915 E(BOND)=227.667 E(ANGL)=393.668 | | E(DIHE)=0.000 E(IMPR)=90.161 E(VDW )=-214.826 E(ELEC)=-135.054 | | E(CDIH)=13.846 E(NOE )=143.017 E(PLAN)=17.474 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63279 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63219 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63173 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63165 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63183 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63214 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63261 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=1160.020 E(kin)=613.317 temperature=303.925 | | Etotal =546.702 grad(E)=69.982 E(BOND)=224.834 E(ANGL)=415.359 | | E(DIHE)=0.000 E(IMPR)=99.387 E(VDW )=-233.372 E(ELEC)=-134.130 | | E(CDIH)=16.311 E(NOE )=140.752 E(PLAN)=17.561 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63277 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63335 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63384 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63382 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63399 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63342 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=1142.313 E(kin)=605.969 temperature=300.283 | | Etotal =536.344 grad(E)=70.558 E(BOND)=256.706 E(ANGL)=368.476 | | E(DIHE)=0.000 E(IMPR)=94.070 E(VDW )=-224.267 E(ELEC)=-132.690 | | E(CDIH)=18.125 E(NOE )=141.868 E(PLAN)=14.056 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63246 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63258 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63216 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63218 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63218 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63108 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63112 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=1148.668 E(kin)=610.694 temperature=302.625 | | Etotal =537.974 grad(E)=66.085 E(BOND)=219.963 E(ANGL)=412.783 | | E(DIHE)=0.000 E(IMPR)=109.559 E(VDW )=-228.089 E(ELEC)=-129.486 | | E(CDIH)=14.818 E(NOE )=126.366 E(PLAN)=12.060 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63045 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 -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63014 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62993 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62993 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=1128.462 E(kin)=619.670 temperature=307.073 | | Etotal =508.792 grad(E)=65.028 E(BOND)=204.027 E(ANGL)=422.786 | | E(DIHE)=0.000 E(IMPR)=84.761 E(VDW )=-227.191 E(ELEC)=-140.242 | | E(CDIH)=21.360 E(NOE )=127.948 E(PLAN)=15.343 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63040 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62993 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62970 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62858 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62743 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62679 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62612 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=1135.864 E(kin)=609.823 temperature=302.193 | | Etotal =526.041 grad(E)=67.375 E(BOND)=209.844 E(ANGL)=404.347 | | E(DIHE)=0.000 E(IMPR)=99.227 E(VDW )=-209.959 E(ELEC)=-139.118 | | E(CDIH)=20.976 E(NOE )=120.795 E(PLAN)=19.928 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62642 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62680 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62756 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62782 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62765 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=1129.288 E(kin)=594.023 temperature=294.363 | | Etotal =535.265 grad(E)=67.098 E(BOND)=232.946 E(ANGL)=432.880 | | E(DIHE)=0.000 E(IMPR)=89.054 E(VDW )=-229.593 E(ELEC)=-140.131 | | E(CDIH)=14.246 E(NOE )=115.958 E(PLAN)=19.906 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1148.389 E(kin)=605.651 temperature=300.125 | | Etotal =542.738 grad(E)=68.641 E(BOND)=226.342 E(ANGL)=408.203 | | E(DIHE)=0.000 E(IMPR)=97.959 E(VDW )=-222.502 E(ELEC)=-133.692 | | E(CDIH)=19.255 E(NOE )=130.731 E(PLAN)=16.442 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.080 E(kin)=12.434 temperature=6.162 | | Etotal =16.191 grad(E)=1.461 E(BOND)=10.743 E(ANGL)=13.593 | | E(DIHE)=0.000 E(IMPR)=7.184 E(VDW )=7.363 E(ELEC)=4.374 | | E(CDIH)=4.352 E(NOE )=9.496 E(PLAN)=2.116 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=1147.740 E(kin)=605.285 temperature=299.944 | | Etotal =542.455 grad(E)=66.674 E(BOND)=215.972 E(ANGL)=408.283 | | E(DIHE)=0.000 E(IMPR)=96.689 E(VDW )=-217.173 E(ELEC)=-133.492 | | E(CDIH)=19.389 E(NOE )=136.164 E(PLAN)=16.624 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=18.109 E(kin)=13.641 temperature=6.760 | | Etotal =19.472 grad(E)=2.107 E(BOND)=12.393 E(ANGL)=14.095 | | E(DIHE)=0.000 E(IMPR)=7.169 E(VDW )=9.622 E(ELEC)=6.242 | | E(CDIH)=5.068 E(NOE )=11.619 E(PLAN)=2.127 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62779 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62812 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62766 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62831 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62860 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=1143.926 E(kin)=612.058 temperature=303.301 | | Etotal =531.867 grad(E)=67.544 E(BOND)=214.452 E(ANGL)=414.240 | | E(DIHE)=0.000 E(IMPR)=104.370 E(VDW )=-220.500 E(ELEC)=-142.246 | | E(CDIH)=17.226 E(NOE )=131.467 E(PLAN)=12.858 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62832 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62891 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62859 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62921 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62959 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63058 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=1156.402 E(kin)=607.290 temperature=300.938 | | Etotal =549.112 grad(E)=68.243 E(BOND)=231.160 E(ANGL)=411.476 | | E(DIHE)=0.000 E(IMPR)=86.513 E(VDW )=-210.077 E(ELEC)=-141.438 | | E(CDIH)=14.514 E(NOE )=138.102 E(PLAN)=18.862 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63132 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63111 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63224 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63233 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63200 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63239 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63247 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=1154.305 E(kin)=619.945 temperature=307.209 | | Etotal =534.359 grad(E)=69.249 E(BOND)=230.100 E(ANGL)=397.940 | | E(DIHE)=0.000 E(IMPR)=96.242 E(VDW )=-220.265 E(ELEC)=-142.377 | | E(CDIH)=20.867 E(NOE )=136.005 E(PLAN)=15.848 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63224 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63217 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63188 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63154 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63094 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63122 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63128 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=1150.536 E(kin)=595.157 temperature=294.925 | | Etotal =555.379 grad(E)=69.205 E(BOND)=238.250 E(ANGL)=421.485 | | E(DIHE)=0.000 E(IMPR)=87.485 E(VDW )=-219.828 E(ELEC)=-140.059 | | E(CDIH)=15.354 E(NOE )=134.514 E(PLAN)=18.177 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63149 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63118 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63123 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63101 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63140 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63136 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63160 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63167 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=1157.239 E(kin)=598.068 temperature=296.368 | | Etotal =559.171 grad(E)=69.881 E(BOND)=233.490 E(ANGL)=396.516 | | E(DIHE)=0.000 E(IMPR)=95.103 E(VDW )=-207.244 E(ELEC)=-135.817 | | E(CDIH)=23.018 E(NOE )=138.861 E(PLAN)=15.245 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 63208 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.40 A apart NBONDS: found 63116 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63121 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63030 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62984 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 -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63008 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62957 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62942 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62913 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=1160.706 E(kin)=599.044 temperature=296.852 | | Etotal =561.661 grad(E)=67.401 E(BOND)=234.934 E(ANGL)=410.165 | | E(DIHE)=0.000 E(IMPR)=97.228 E(VDW )=-211.363 E(ELEC)=-131.077 | | E(CDIH)=13.213 E(NOE )=135.980 E(PLAN)=12.581 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62980 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63015 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63084 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63111 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63126 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63132 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63102 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63081 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 63075 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=1158.122 E(kin)=603.146 temperature=298.884 | | Etotal =554.976 grad(E)=68.307 E(BOND)=236.599 E(ANGL)=404.607 | | E(DIHE)=0.000 E(IMPR)=99.091 E(VDW )=-230.900 E(ELEC)=-141.720 | | E(CDIH)=15.391 E(NOE )=156.605 E(PLAN)=15.304 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63076 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63074 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63071 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " 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 63115 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63187 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63167 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=1149.285 E(kin)=605.756 temperature=300.177 | | Etotal =543.529 grad(E)=71.406 E(BOND)=228.095 E(ANGL)=405.031 | | E(DIHE)=0.000 E(IMPR)=94.748 E(VDW )=-203.429 E(ELEC)=-140.766 | | E(CDIH)=15.895 E(NOE )=127.126 E(PLAN)=16.830 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63188 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 -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63161 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63131 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63109 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63047 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63017 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62972 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63027 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=1148.909 E(kin)=623.200 temperature=308.822 | | Etotal =525.710 grad(E)=66.707 E(BOND)=220.287 E(ANGL)=401.825 | | E(DIHE)=0.000 E(IMPR)=87.012 E(VDW )=-214.933 E(ELEC)=-141.827 | | E(CDIH)=15.672 E(NOE )=137.482 E(PLAN)=20.191 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 63025 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 63039 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63025 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62989 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " 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 63002 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " 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 63013 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=1162.766 E(kin)=614.039 temperature=304.282 | | Etotal =548.727 grad(E)=66.332 E(BOND)=224.360 E(ANGL)=418.941 | | E(DIHE)=0.000 E(IMPR)=94.315 E(VDW )=-226.479 E(ELEC)=-132.639 | | E(CDIH)=13.358 E(NOE )=140.971 E(PLAN)=15.901 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1151.551 E(kin)=605.358 temperature=299.980 | | Etotal =546.193 grad(E)=68.576 E(BOND)=226.595 E(ANGL)=413.415 | | E(DIHE)=0.000 E(IMPR)=94.627 E(VDW )=-217.565 E(ELEC)=-139.729 | | E(CDIH)=17.878 E(NOE )=134.705 E(PLAN)=16.267 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.070 E(kin)=12.659 temperature=6.273 | | Etotal =15.131 grad(E)=1.422 E(BOND)=10.315 E(ANGL)=12.964 | | E(DIHE)=0.000 E(IMPR)=7.051 E(VDW )=6.652 E(ELEC)=3.497 | | E(CDIH)=3.906 E(NOE )=9.445 E(PLAN)=2.147 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=1148.057 E(kin)=605.291 temperature=299.947 | | Etotal =542.766 grad(E)=66.832 E(BOND)=216.858 E(ANGL)=408.711 | | E(DIHE)=0.000 E(IMPR)=96.517 E(VDW )=-217.206 E(ELEC)=-134.012 | | E(CDIH)=19.263 E(NOE )=136.043 E(PLAN)=16.594 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=17.566 E(kin)=13.562 temperature=6.721 | | Etotal =19.176 grad(E)=2.125 E(BOND)=12.581 E(ANGL)=14.076 | | E(DIHE)=0.000 E(IMPR)=7.182 E(VDW )=9.411 E(ELEC)=6.302 | | E(CDIH)=4.999 E(NOE )=11.461 E(PLAN)=2.130 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63007 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63067 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63103 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63154 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63151 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63118 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.23 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63103 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=1157.832 E(kin)=611.152 temperature=302.852 | | Etotal =546.680 grad(E)=67.119 E(BOND)=223.305 E(ANGL)=432.116 | | E(DIHE)=0.000 E(IMPR)=92.983 E(VDW )=-222.695 E(ELEC)=-136.130 | | E(CDIH)=16.680 E(NOE )=125.887 E(PLAN)=14.533 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63075 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63070 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63074 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63046 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63019 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63097 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 -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63124 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=1160.550 E(kin)=623.784 temperature=309.111 | | Etotal =536.767 grad(E)=67.883 E(BOND)=218.268 E(ANGL)=404.144 | | E(DIHE)=0.000 E(IMPR)=100.980 E(VDW )=-219.326 E(ELEC)=-140.249 | | E(CDIH)=23.182 E(NOE )=129.657 E(PLAN)=20.111 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63115 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63149 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63088 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63081 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63010 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.22 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62996 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62964 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62941 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=1142.762 E(kin)=595.234 temperature=294.963 | | Etotal =547.528 grad(E)=69.160 E(BOND)=214.289 E(ANGL)=417.501 | | E(DIHE)=0.000 E(IMPR)=96.651 E(VDW )=-211.471 E(ELEC)=-135.969 | | E(CDIH)=26.975 E(NOE )=122.985 E(PLAN)=16.567 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62884 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 62826 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 62806 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 62777 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62702 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62648 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62736 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62797 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=1143.307 E(kin)=613.250 temperature=303.891 | | Etotal =530.057 grad(E)=68.813 E(BOND)=212.826 E(ANGL)=409.560 | | E(DIHE)=0.000 E(IMPR)=95.653 E(VDW )=-222.350 E(ELEC)=-127.019 | | E(CDIH)=14.821 E(NOE )=132.313 E(PLAN)=14.253 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62893 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62936 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62922 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 62916 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 62854 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62866 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62859 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 62856 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=1147.970 E(kin)=613.499 temperature=304.014 | | Etotal =534.471 grad(E)=70.303 E(BOND)=221.943 E(ANGL)=400.679 | | E(DIHE)=0.000 E(IMPR)=94.338 E(VDW )=-219.912 E(ELEC)=-130.850 | | E(CDIH)=21.584 E(NOE )=129.653 E(PLAN)=17.036 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62897 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62861 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 62846 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62902 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62778 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62769 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62760 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62731 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=1146.437 E(kin)=600.090 temperature=297.370 | | Etotal =546.346 grad(E)=68.900 E(BOND)=234.406 E(ANGL)=404.855 | | E(DIHE)=0.000 E(IMPR)=96.850 E(VDW )=-228.634 E(ELEC)=-132.209 | | E(CDIH)=19.417 E(NOE )=135.303 E(PLAN)=16.358 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart NBONDS: found 62718 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62713 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 62686 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62670 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62630 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62649 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62634 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=1164.569 E(kin)=598.663 temperature=296.663 | | Etotal =565.906 grad(E)=69.395 E(BOND)=228.645 E(ANGL)=410.993 | | E(DIHE)=0.000 E(IMPR)=99.077 E(VDW )=-224.296 E(ELEC)=-128.266 | | E(CDIH)=23.196 E(NOE )=143.470 E(PLAN)=13.087 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 62656 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 62654 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62600 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.44 A apart NBONDS: found 62643 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62653 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62652 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62703 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.22 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62735 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=1155.539 E(kin)=615.332 temperature=304.923 | | Etotal =540.208 grad(E)=69.835 E(BOND)=207.751 E(ANGL)=406.423 | | E(DIHE)=0.000 E(IMPR)=95.053 E(VDW )=-215.898 E(ELEC)=-130.952 | | E(CDIH)=28.354 E(NOE )=133.594 E(PLAN)=15.883 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.42 A apart NBONDS: found 62811 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 62861 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62853 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62831 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62721 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62626 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62545 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=1157.932 E(kin)=584.410 temperature=289.600 | | Etotal =573.522 grad(E)=72.090 E(BOND)=238.519 E(ANGL)=420.589 | | E(DIHE)=0.000 E(IMPR)=97.934 E(VDW )=-231.377 E(ELEC)=-126.553 | | E(CDIH)=16.160 E(NOE )=140.849 E(PLAN)=17.401 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62482 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62446 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 62497 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 62697 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 62828 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=1141.840 E(kin)=602.927 temperature=298.775 | | Etotal =538.913 grad(E)=71.609 E(BOND)=213.160 E(ANGL)=405.571 | | E(DIHE)=0.000 E(IMPR)=103.065 E(VDW )=-221.220 E(ELEC)=-137.434 | | E(CDIH)=16.663 E(NOE )=142.326 E(PLAN)=16.783 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1150.734 E(kin)=605.575 temperature=300.088 | | Etotal =545.159 grad(E)=68.683 E(BOND)=223.521 E(ANGL)=411.994 | | E(DIHE)=0.000 E(IMPR)=96.885 E(VDW )=-222.810 E(ELEC)=-131.224 | | E(CDIH)=19.577 E(NOE )=131.252 E(PLAN)=15.964 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.399 E(kin)=12.676 temperature=6.281 | | Etotal =14.754 grad(E)=1.460 E(BOND)=10.234 E(ANGL)=12.885 | | E(DIHE)=0.000 E(IMPR)=6.652 E(VDW )=6.622 E(ELEC)=4.721 | | E(CDIH)=4.178 E(NOE )=8.167 E(PLAN)=2.204 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=1148.263 E(kin)=605.313 temperature=299.958 | | Etotal =542.950 grad(E)=66.975 E(BOND)=217.370 E(ANGL)=408.963 | | E(DIHE)=0.000 E(IMPR)=96.545 E(VDW )=-217.637 E(ELEC)=-133.798 | | E(CDIH)=19.287 E(NOE )=135.674 E(PLAN)=16.546 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=17.052 E(kin)=13.496 temperature=6.688 | | Etotal =18.884 grad(E)=2.139 E(BOND)=12.542 E(ANGL)=14.015 | | E(DIHE)=0.000 E(IMPR)=7.143 E(VDW )=9.347 E(ELEC)=6.239 | | E(CDIH)=4.942 E(NOE )=11.314 E(PLAN)=2.143 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 62925 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63007 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63013 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63006 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62929 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 62971 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62941 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=1129.902 E(kin)=603.213 temperature=298.917 | | Etotal =526.689 grad(E)=67.691 E(BOND)=215.896 E(ANGL)=411.603 | | E(DIHE)=0.000 E(IMPR)=75.939 E(VDW )=-229.614 E(ELEC)=-130.779 | | E(CDIH)=28.479 E(NOE )=139.997 E(PLAN)=15.169 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62906 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62844 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 62835 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62816 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62789 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=1137.296 E(kin)=579.750 temperature=287.290 | | Etotal =557.546 grad(E)=71.214 E(BOND)=229.985 E(ANGL)=412.350 | | E(DIHE)=0.000 E(IMPR)=90.753 E(VDW )=-226.042 E(ELEC)=-129.449 | | E(CDIH)=16.841 E(NOE )=146.583 E(PLAN)=16.524 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62821 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 62957 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63069 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63126 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63279 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " 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 63280 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63310 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=1156.186 E(kin)=583.218 temperature=289.009 | | Etotal =572.968 grad(E)=69.897 E(BOND)=259.363 E(ANGL)=411.153 | | E(DIHE)=0.000 E(IMPR)=85.838 E(VDW )=-220.162 E(ELEC)=-144.719 | | E(CDIH)=18.532 E(NOE )=142.934 E(PLAN)=20.028 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63243 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63163 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63108 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63088 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63042 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62956 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62923 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=1141.809 E(kin)=608.616 temperature=301.595 | | Etotal =533.194 grad(E)=67.744 E(BOND)=231.966 E(ANGL)=393.783 | | E(DIHE)=0.000 E(IMPR)=92.184 E(VDW )=-226.444 E(ELEC)=-129.558 | | E(CDIH)=19.265 E(NOE )=133.062 E(PLAN)=18.935 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 62906 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 -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62899 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 -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62931 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62955 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62936 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 62934 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 62960 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63035 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63053 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63015 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=1150.075 E(kin)=611.465 temperature=303.006 | | Etotal =538.610 grad(E)=67.231 E(BOND)=222.888 E(ANGL)=395.854 | | E(DIHE)=0.000 E(IMPR)=101.988 E(VDW )=-208.282 E(ELEC)=-126.598 | | E(CDIH)=15.065 E(NOE )=121.591 E(PLAN)=16.105 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63011 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 62982 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63026 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63034 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63044 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 63038 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63042 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63067 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63099 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63084 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63058 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=1153.244 E(kin)=625.906 temperature=310.163 | | Etotal =527.338 grad(E)=65.894 E(BOND)=219.405 E(ANGL)=406.100 | | E(DIHE)=0.000 E(IMPR)=79.286 E(VDW )=-208.316 E(ELEC)=-135.756 | | E(CDIH)=18.978 E(NOE )=128.597 E(PLAN)=19.044 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63045 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63072 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63054 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63056 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63090 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63163 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63247 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63241 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63378 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=1152.684 E(kin)=613.822 temperature=304.174 | | Etotal =538.862 grad(E)=67.221 E(BOND)=231.369 E(ANGL)=403.601 | | E(DIHE)=0.000 E(IMPR)=90.091 E(VDW )=-206.400 E(ELEC)=-136.380 | | E(CDIH)=12.231 E(NOE )=127.674 E(PLAN)=16.676 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63479 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63529 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63512 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63583 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63650 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63719 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63755 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=1154.645 E(kin)=594.606 temperature=294.652 | | Etotal =560.039 grad(E)=71.190 E(BOND)=237.540 E(ANGL)=390.554 | | E(DIHE)=0.000 E(IMPR)=115.982 E(VDW )=-204.622 E(ELEC)=-130.240 | | E(CDIH)=19.477 E(NOE )=114.531 E(PLAN)=16.817 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63761 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 -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63738 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 -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63754 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63734 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63797 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63799 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=1153.302 E(kin)=597.136 temperature=295.906 | | Etotal =556.165 grad(E)=68.511 E(BOND)=235.589 E(ANGL)=400.014 | | E(DIHE)=0.000 E(IMPR)=99.221 E(VDW )=-220.352 E(ELEC)=-130.865 | | E(CDIH)=15.726 E(NOE )=138.230 E(PLAN)=18.603 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart NBONDS: found 63797 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart NBONDS: found 63730 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63685 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.30 A apart NBONDS: found 63679 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63663 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63667 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63635 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63677 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 63674 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=1164.320 E(kin)=609.544 temperature=302.055 | | Etotal =554.776 grad(E)=69.312 E(BOND)=217.845 E(ANGL)=418.483 | | E(DIHE)=0.000 E(IMPR)=102.969 E(VDW )=-217.451 E(ELEC)=-140.307 | | E(CDIH)=15.636 E(NOE )=141.903 E(PLAN)=15.699 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1152.079 E(kin)=605.395 temperature=299.999 | | Etotal =546.684 grad(E)=68.546 E(BOND)=225.515 E(ANGL)=409.384 | | E(DIHE)=0.000 E(IMPR)=94.974 E(VDW )=-218.375 E(ELEC)=-132.600 | | E(CDIH)=17.949 E(NOE )=133.239 E(PLAN)=16.598 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.948 E(kin)=12.691 temperature=6.289 | | Etotal =15.700 grad(E)=1.424 E(BOND)=10.762 E(ANGL)=12.538 | | E(DIHE)=0.000 E(IMPR)=7.448 E(VDW )=7.869 E(ELEC)=4.921 | | E(CDIH)=4.286 E(NOE )=10.554 E(PLAN)=1.890 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=1148.536 E(kin)=605.319 temperature=299.961 | | Etotal =543.217 grad(E)=67.087 E(BOND)=217.952 E(ANGL)=408.993 | | E(DIHE)=0.000 E(IMPR)=96.433 E(VDW )=-217.690 E(ELEC)=-133.712 | | E(CDIH)=19.191 E(NOE )=135.500 E(PLAN)=16.549 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=16.675 E(kin)=13.440 temperature=6.660 | | Etotal =18.699 grad(E)=2.135 E(BOND)=12.600 E(ANGL)=13.916 | | E(DIHE)=0.000 E(IMPR)=7.177 E(VDW )=9.251 E(ELEC)=6.162 | | E(CDIH)=4.910 E(NOE )=11.279 E(PLAN)=2.126 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 63687 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63671 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63631 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.23 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63546 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63517 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63558 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63503 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63443 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=1156.250 E(kin)=581.857 temperature=288.335 | | Etotal =574.393 grad(E)=70.184 E(BOND)=240.094 E(ANGL)=406.995 | | E(DIHE)=0.000 E(IMPR)=101.573 E(VDW )=-218.551 E(ELEC)=-140.547 | | E(CDIH)=15.693 E(NOE )=151.381 E(PLAN)=17.756 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63478 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63465 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63481 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63410 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63340 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=1159.103 E(kin)=607.335 temperature=300.960 | | Etotal =551.768 grad(E)=68.813 E(BOND)=219.033 E(ANGL)=408.761 | | E(DIHE)=0.000 E(IMPR)=94.412 E(VDW )=-210.404 E(ELEC)=-135.228 | | E(CDIH)=13.129 E(NOE )=141.658 E(PLAN)=20.407 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " 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 63353 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63376 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63479 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63570 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 -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63615 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63674 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=1153.635 E(kin)=611.983 temperature=303.264 | | Etotal =541.652 grad(E)=66.508 E(BOND)=229.314 E(ANGL)=397.748 | | E(DIHE)=0.000 E(IMPR)=96.262 E(VDW )=-217.128 E(ELEC)=-135.856 | | E(CDIH)=16.991 E(NOE )=135.118 E(PLAN)=19.202 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63760 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " 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 63759 intra-atom interactions %atoms "A -12 -URI -O3' " 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 63808 intra-atom interactions %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63805 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63835 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=1150.484 E(kin)=615.460 temperature=304.986 | | Etotal =535.024 grad(E)=68.264 E(BOND)=221.220 E(ANGL)=406.953 | | E(DIHE)=0.000 E(IMPR)=94.548 E(VDW )=-210.307 E(ELEC)=-133.431 | | E(CDIH)=10.529 E(NOE )=130.529 E(PLAN)=14.982 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63819 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63897 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63882 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63894 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 63890 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63904 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=1152.524 E(kin)=617.348 temperature=305.922 | | Etotal =535.175 grad(E)=68.188 E(BOND)=223.474 E(ANGL)=394.700 | | E(DIHE)=0.000 E(IMPR)=93.967 E(VDW )=-227.648 E(ELEC)=-139.737 | | E(CDIH)=27.710 E(NOE )=146.568 E(PLAN)=16.141 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63962 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63947 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63889 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63879 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63818 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63887 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63894 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=1150.202 E(kin)=607.774 temperature=301.177 | | Etotal =542.428 grad(E)=69.281 E(BOND)=227.445 E(ANGL)=412.840 | | E(DIHE)=0.000 E(IMPR)=92.105 E(VDW )=-214.727 E(ELEC)=-137.849 | | E(CDIH)=24.177 E(NOE )=122.427 E(PLAN)=16.010 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64039 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64093 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64105 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 64119 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 64147 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 -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 64133 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64155 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=1167.963 E(kin)=603.944 temperature=299.280 | | Etotal =564.019 grad(E)=71.003 E(BOND)=216.490 E(ANGL)=443.354 | | E(DIHE)=0.000 E(IMPR)=90.475 E(VDW )=-208.883 E(ELEC)=-137.371 | | E(CDIH)=13.364 E(NOE )=128.844 E(PLAN)=17.746 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 64163 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 64142 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64122 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 64051 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 64018 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=1141.191 E(kin)=588.616 temperature=291.684 | | Etotal =552.575 grad(E)=70.309 E(BOND)=229.396 E(ANGL)=419.036 | | E(DIHE)=0.000 E(IMPR)=108.492 E(VDW )=-223.837 E(ELEC)=-138.821 | | E(CDIH)=19.996 E(NOE )=123.272 E(PLAN)=15.040 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 64001 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63940 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.35 A apart NBONDS: found 63790 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63740 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 63613 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63485 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63392 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=1161.663 E(kin)=615.512 temperature=305.012 | | Etotal =546.150 grad(E)=67.967 E(BOND)=221.785 E(ANGL)=407.515 | | E(DIHE)=0.000 E(IMPR)=96.666 E(VDW )=-218.718 E(ELEC)=-135.975 | | E(CDIH)=17.959 E(NOE )=141.556 E(PLAN)=15.362 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 63369 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63388 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 -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 63333 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.29 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63272 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63201 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63180 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=1142.035 E(kin)=600.617 temperature=297.631 | | Etotal =541.419 grad(E)=67.604 E(BOND)=219.010 E(ANGL)=427.297 | | E(DIHE)=0.000 E(IMPR)=102.936 E(VDW )=-223.950 E(ELEC)=-136.100 | | E(CDIH)=16.745 E(NOE )=122.336 E(PLAN)=13.146 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1151.531 E(kin)=605.577 temperature=300.089 | | Etotal =545.954 grad(E)=68.279 E(BOND)=224.986 E(ANGL)=410.158 | | E(DIHE)=0.000 E(IMPR)=96.195 E(VDW )=-217.203 E(ELEC)=-137.315 | | E(CDIH)=16.670 E(NOE )=136.281 E(PLAN)=16.181 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.993 E(kin)=13.072 temperature=6.478 | | Etotal =15.402 grad(E)=1.495 E(BOND)=10.045 E(ANGL)=12.607 | | E(DIHE)=0.000 E(IMPR)=6.818 E(VDW )=8.395 E(ELEC)=3.866 | | E(CDIH)=4.275 E(NOE )=8.651 E(PLAN)=1.769 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=1148.735 E(kin)=605.336 temperature=299.969 | | Etotal =543.399 grad(E)=67.167 E(BOND)=218.421 E(ANGL)=409.071 | | E(DIHE)=0.000 E(IMPR)=96.417 E(VDW )=-217.657 E(ELEC)=-133.952 | | E(CDIH)=19.023 E(NOE )=135.552 E(PLAN)=16.525 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=16.293 E(kin)=13.416 temperature=6.648 | | Etotal =18.510 grad(E)=2.119 E(BOND)=12.569 E(ANGL)=13.835 | | E(DIHE)=0.000 E(IMPR)=7.154 E(VDW )=9.197 E(ELEC)=6.102 | | E(CDIH)=4.911 E(NOE )=11.125 E(PLAN)=2.106 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63146 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63132 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63096 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63074 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63119 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63214 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=1150.396 E(kin)=610.866 temperature=302.710 | | Etotal =539.530 grad(E)=68.181 E(BOND)=228.811 E(ANGL)=397.344 | | E(DIHE)=0.000 E(IMPR)=106.836 E(VDW )=-216.072 E(ELEC)=-139.688 | | E(CDIH)=23.575 E(NOE )=120.231 E(PLAN)=18.493 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63257 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart NBONDS: found 63209 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63119 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63086 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63035 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63035 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.24 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63131 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=1154.858 E(kin)=603.372 temperature=298.996 | | Etotal =551.486 grad(E)=69.692 E(BOND)=238.240 E(ANGL)=408.419 | | E(DIHE)=0.000 E(IMPR)=96.482 E(VDW )=-215.350 E(ELEC)=-140.981 | | E(CDIH)=21.235 E(NOE )=124.493 E(PLAN)=18.949 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63178 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63262 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63332 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.26 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63361 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63433 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.32 A apart NBONDS: found 63508 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63528 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=1156.728 E(kin)=609.617 temperature=302.091 | | Etotal =547.111 grad(E)=70.223 E(BOND)=226.066 E(ANGL)=424.816 | | E(DIHE)=0.000 E(IMPR)=99.962 E(VDW )=-234.440 E(ELEC)=-132.885 | | E(CDIH)=12.531 E(NOE )=135.365 E(PLAN)=15.696 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63565 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63563 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 63545 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63503 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63483 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 63489 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=1141.894 E(kin)=608.729 temperature=301.651 | | Etotal =533.165 grad(E)=65.504 E(BOND)=231.544 E(ANGL)=392.868 | | E(DIHE)=0.000 E(IMPR)=84.195 E(VDW )=-226.927 E(ELEC)=-132.529 | | E(CDIH)=26.605 E(NOE )=140.853 E(PLAN)=16.557 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 63502 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.37 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63480 intra-atom interactions %atoms "A -8 -CYT -O2' " and "A -11 -ADE -HO2'" only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63545 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 63497 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63666 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=1146.886 E(kin)=624.029 temperature=309.233 | | Etotal =522.857 grad(E)=67.246 E(BOND)=209.362 E(ANGL)=415.181 | | E(DIHE)=0.000 E(IMPR)=92.060 E(VDW )=-211.933 E(ELEC)=-136.255 | | E(CDIH)=18.863 E(NOE )=120.291 E(PLAN)=15.288 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63623 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63657 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 63537 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.33 A apart NBONDS: found 63493 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63484 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63440 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63445 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=1161.714 E(kin)=617.487 temperature=305.991 | | Etotal =544.227 grad(E)=66.297 E(BOND)=229.428 E(ANGL)=403.247 | | E(DIHE)=0.000 E(IMPR)=93.885 E(VDW )=-212.411 E(ELEC)=-136.628 | | E(CDIH)=21.477 E(NOE )=125.018 E(PLAN)=20.212 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63397 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63378 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 -11 -ADE -H5' " only 1.32 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63336 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63313 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63284 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63299 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=1141.186 E(kin)=600.179 temperature=297.414 | | Etotal =541.007 grad(E)=66.373 E(BOND)=228.760 E(ANGL)=412.740 | | E(DIHE)=0.000 E(IMPR)=90.784 E(VDW )=-216.684 E(ELEC)=-134.846 | | E(CDIH)=9.357 E(NOE )=129.479 E(PLAN)=21.418 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.33 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63278 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.36 A apart NBONDS: found 63246 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63252 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 63199 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63158 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63114 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=1134.458 E(kin)=597.354 temperature=296.014 | | Etotal =537.104 grad(E)=68.917 E(BOND)=229.841 E(ANGL)=402.290 | | E(DIHE)=0.000 E(IMPR)=101.490 E(VDW )=-231.570 E(ELEC)=-132.076 | | E(CDIH)=19.268 E(NOE )=132.163 E(PLAN)=15.699 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63032 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.40 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 62949 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.37 A apart NBONDS: found 62884 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.28 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 62979 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.31 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63061 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 63094 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 63172 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.38 A apart NBONDS: found 63216 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=1172.594 E(kin)=613.011 temperature=303.773 | | Etotal =559.583 grad(E)=67.591 E(BOND)=234.000 E(ANGL)=419.315 | | E(DIHE)=0.000 E(IMPR)=88.239 E(VDW )=-214.892 E(ELEC)=-130.733 | | E(CDIH)=14.706 E(NOE )=135.035 E(PLAN)=13.912 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 63290 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63308 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63624 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=1148.227 E(kin)=595.124 temperature=294.909 | | Etotal =553.104 grad(E)=67.772 E(BOND)=229.014 E(ANGL)=415.075 | | E(DIHE)=0.000 E(IMPR)=96.232 E(VDW )=-207.198 E(ELEC)=-136.542 | | E(CDIH)=14.256 E(NOE )=126.174 E(PLAN)=16.094 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1152.027 E(kin)=605.448 temperature=300.025 | | Etotal =546.579 grad(E)=68.276 E(BOND)=228.609 E(ANGL)=410.253 | | E(DIHE)=0.000 E(IMPR)=93.793 E(VDW )=-220.499 E(ELEC)=-134.800 | | E(CDIH)=19.690 E(NOE )=132.864 E(PLAN)=16.668 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.009 E(kin)=12.197 temperature=6.044 | | Etotal =15.383 grad(E)=1.440 E(BOND)=10.244 E(ANGL)=12.873 | | E(DIHE)=0.000 E(IMPR)=6.896 E(VDW )=7.825 E(ELEC)=3.969 | | E(CDIH)=4.877 E(NOE )=9.004 E(PLAN)=2.226 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=1148.941 E(kin)=605.343 temperature=299.973 | | Etotal =543.598 grad(E)=67.236 E(BOND)=219.058 E(ANGL)=409.145 | | E(DIHE)=0.000 E(IMPR)=96.253 E(VDW )=-217.835 E(ELEC)=-134.005 | | E(CDIH)=19.065 E(NOE )=135.384 E(PLAN)=16.534 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=15.993 E(kin)=13.343 temperature=6.612 | | Etotal =18.346 grad(E)=2.100 E(BOND)=12.678 E(ANGL)=13.780 | | E(DIHE)=0.000 E(IMPR)=7.166 E(VDW )=9.143 E(ELEC)=5.995 | | E(CDIH)=4.911 E(NOE )=11.024 E(PLAN)=2.114 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : -0.09840 -0.02551 0.00097 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 04:33:39 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 -O2' " and "A -11 -ADE -H5' " only 1.35 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63385 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.25 A apart %atoms "A -12 -URI -O3' " and "A -13 -ADE -H8 " only 1.40 A apart NBONDS: found 63376 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =-33.200 grad(E)=7.250 E(BOND)=20.425 E(ANGL)=162.182 | | E(DIHE)=0.000 E(IMPR)=20.795 E(VDW )=-220.112 E(ELEC)=-138.441 | | E(CDIH)=15.738 E(NOE )=91.997 E(PLAN)=14.216 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =-54.310 grad(E)=3.410 E(BOND)=13.980 E(ANGL)=152.397 | | E(DIHE)=0.000 E(IMPR)=19.750 E(VDW )=-224.793 E(ELEC)=-138.423 | | E(CDIH)=15.927 E(NOE )=93.362 E(PLAN)=13.490 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =-61.252 grad(E)=2.256 E(BOND)=12.896 E(ANGL)=148.530 | | E(DIHE)=0.000 E(IMPR)=19.017 E(VDW )=-228.783 E(ELEC)=-139.754 | | E(CDIH)=15.644 E(NOE )=98.590 E(PLAN)=12.607 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =-63.366 grad(E)=1.209 E(BOND)=13.186 E(ANGL)=147.178 | | E(DIHE)=0.000 E(IMPR)=19.132 E(VDW )=-230.300 E(ELEC)=-141.104 | | E(CDIH)=15.453 E(NOE )=100.836 E(PLAN)=12.253 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =-64.829 grad(E)=1.654 E(BOND)=13.122 E(ANGL)=146.406 | | E(DIHE)=0.000 E(IMPR)=18.801 E(VDW )=-231.547 E(ELEC)=-142.483 | | E(CDIH)=15.197 E(NOE )=103.659 E(PLAN)=12.016 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =-65.826 grad(E)=1.151 E(BOND)=13.034 E(ANGL)=146.098 | | E(DIHE)=0.000 E(IMPR)=18.406 E(VDW )=-231.711 E(ELEC)=-143.140 | | E(CDIH)=15.240 E(NOE )=104.313 E(PLAN)=11.934 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =-66.756 grad(E)=0.883 E(BOND)=12.903 E(ANGL)=145.386 | | E(DIHE)=0.000 E(IMPR)=18.335 E(VDW )=-231.397 E(ELEC)=-144.289 | | E(CDIH)=14.973 E(NOE )=105.353 E(PLAN)=11.980 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =-67.430 grad(E)=0.704 E(BOND)=12.979 E(ANGL)=145.228 | | E(DIHE)=0.000 E(IMPR)=18.476 E(VDW )=-230.480 E(ELEC)=-145.001 | | E(CDIH)=14.746 E(NOE )=104.509 E(PLAN)=12.111 | ------------------------------------------------------------------------------- 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. Number of violations greater 0.050: 0 RMS deviation= 0.003 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.294858E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (A 12 C4' |A 12 C3' |A 12 O3' ) 116.797 110.500 6.297 5.375 445.032 (A 12 C1' |A 12 C2' |A 12 O2' ) 105.096 110.600 -5.504 3.301 357.719 (A 12 O3' |A 13 P |A 13 O5' ) 95.818 104.000 -8.182 16.994 833.356 Number of violations greater 5.000: 3 RMS deviation= 0.818 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.817938 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 3.00000 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.453 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.453240 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 9 URI H2' set-j-atoms A 11 ADE H8 R= 4.585 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.585 E(NOE)= 34.212 ======================================== set-i-atoms A 10 CYT H1' set-j-atoms A 11 ADE H8 R= 5.297 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.297 E(NOE)= 8.823 ======================================== set-i-atoms A 11 ADE H8 set-j-atoms A 12 URI H6 R= 5.209 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.209 E(NOE)= 4.348 ======================================== set-i-atoms A 12 URI H2' set-j-atoms A 13 ADE H1' R= 5.344 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.344 E(NOE)= 11.834 ======================================== set-i-atoms A 12 URI H6 set-j-atoms A 13 ADE H8 R= 5.407 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.407 E(NOE)= 16.588 NOEPRI: RMS diff. = 0.034, #(violat.> 0.2)= 5 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.034, #(viol.> 0.2)= 5 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.335585E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 5.00000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 ======================================== A 13 ADE P A 13 ADE O5' A 13 ADE C5' A 13 ADE C4' Dihedral= 142.714 Energy= 0.009 C= 1.000 Equil= 178.000 Delta= 5.286 Range= 30.000 Exponent= 2 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 1 RMS deviation= 0.546 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.545972 (real) X-PLOR>evaluate ($v_cdih=$violations) EVALUATE: symbol $V_CDIH set to 1.00000 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 12.9795, angle 145.228, dihedral 0, improper 18.4764, NOE 104.509, c-dihedral 14.7462, planar 12.1111, VdW -230.48, elec -145.001, total -67.4298 RMSD: bond 2.948581E-03, angle 0.817938, dihedral 0, improper 0.45324, NOE 3.355854E-02, c-dihedral 0.545972 Violations: bond 0, angle 3, dihedral 0, improper 0, NOE 5, 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= 134787 current use= 0 X-PLOR: total CPU time= 3190.4260 s X-PLOR: entry time at 04:33:06 17-Aug-96 X-PLOR: exit time at 05:26:35 17-Aug-96