X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 05:29:15 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=91676.9715270996 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 19:03:49 created by user: COOR>ATOM 1 P GUA A 1 -8.778 10.833 2.780 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -10.208 11.231 2.727 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 -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.13 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61678 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =37.764 grad(E)=4.734 E(BOND)=17.746 E(ANGL)=152.830 | | E(DIHE)=0.000 E(IMPR)=18.681 E(VDW )=-185.853 E(ELEC)=-98.224 | | E(CDIH)=5.946 E(NOE )=117.088 E(PLAN)=9.550 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =20.217 grad(E)=2.986 E(BOND)=15.301 E(ANGL)=147.415 | | E(DIHE)=0.000 E(IMPR)=15.667 E(VDW )=-192.920 E(ELEC)=-100.256 | | E(CDIH)=4.097 E(NOE )=119.911 E(PLAN)=11.004 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =9.088 grad(E)=3.557 E(BOND)=14.796 E(ANGL)=143.002 | | E(DIHE)=0.000 E(IMPR)=17.552 E(VDW )=-193.073 E(ELEC)=-103.685 | | E(CDIH)=4.471 E(NOE )=115.058 E(PLAN)=10.967 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =-0.573 grad(E)=3.275 E(BOND)=15.992 E(ANGL)=140.096 | | E(DIHE)=0.000 E(IMPR)=18.372 E(VDW )=-197.129 E(ELEC)=-109.299 | | E(CDIH)=5.039 E(NOE )=115.143 E(PLAN)=11.212 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =-6.652 grad(E)=2.084 E(BOND)=15.530 E(ANGL)=138.388 | | E(DIHE)=0.000 E(IMPR)=18.003 E(VDW )=-198.464 E(ELEC)=-113.583 | | E(CDIH)=4.177 E(NOE )=117.792 E(PLAN)=11.504 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =-10.895 grad(E)=1.702 E(BOND)=15.432 E(ANGL)=138.392 | | E(DIHE)=0.000 E(IMPR)=18.798 E(VDW )=-196.440 E(ELEC)=-118.382 | | E(CDIH)=3.329 E(NOE )=116.110 E(PLAN)=11.865 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62045 intra-atom interactions --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =-15.241 grad(E)=2.337 E(BOND)=16.561 E(ANGL)=139.319 | | E(DIHE)=0.000 E(IMPR)=18.315 E(VDW )=-194.142 E(ELEC)=-122.845 | | E(CDIH)=2.955 E(NOE )=112.798 E(PLAN)=11.800 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =-19.582 grad(E)=1.501 E(BOND)=15.590 E(ANGL)=139.280 | | E(DIHE)=0.000 E(IMPR)=18.133 E(VDW )=-190.403 E(ELEC)=-127.294 | | E(CDIH)=3.047 E(NOE )=110.539 E(PLAN)=11.525 | ------------------------------------------------------------------------------- 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= 336864304. ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.08478 0.04526 0.00909 velocity [A/ps] : 0.13564 -0.13400 0.14790 ang. mom. [amu A/ps] : 21378.93474 18247.17911 -13873.00746 kin. ener. [Kcal/mol] : 0.46934 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.08478 0.04526 0.00909 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)=598.791 E(kin)=618.373 temperature=306.430 | | Etotal =-19.582 grad(E)=1.501 E(BOND)=15.590 E(ANGL)=139.280 | | E(DIHE)=0.000 E(IMPR)=18.133 E(VDW )=-190.403 E(ELEC)=-127.294 | | E(CDIH)=3.047 E(NOE )=110.539 E(PLAN)=11.525 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62103 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62087 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.35 A apart NBONDS: found 62053 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.35 A apart NBONDS: found 62035 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62017 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H5' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.35 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62033 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.30 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62010 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 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 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62016 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62041 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62046 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62053 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62050 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=1153.912 E(kin)=586.991 temperature=290.879 | | Etotal =566.921 grad(E)=66.994 E(BOND)=203.248 E(ANGL)=422.307 | | E(DIHE)=0.000 E(IMPR)=78.333 E(VDW )=-178.868 E(ELEC)=-120.871 | | E(CDIH)=4.928 E(NOE )=141.168 E(PLAN)=16.676 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62111 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62147 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart NBONDS: found 62201 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 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 1.48 A apart NBONDS: found 62255 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 62344 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62426 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 62470 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62481 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62465 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62486 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 62485 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 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 1.39 A apart NBONDS: found 62544 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=1164.493 E(kin)=601.674 temperature=298.155 | | Etotal =562.818 grad(E)=66.511 E(BOND)=208.154 E(ANGL)=410.762 | | E(DIHE)=0.000 E(IMPR)=93.788 E(VDW )=-171.286 E(ELEC)=-131.242 | | E(CDIH)=9.690 E(NOE )=121.838 E(PLAN)=21.114 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 62484 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62508 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62514 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 62512 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62534 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62603 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.37 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62665 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62673 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.31 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62745 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=1159.025 E(kin)=616.093 temperature=305.300 | | Etotal =542.931 grad(E)=62.971 E(BOND)=220.943 E(ANGL)=396.887 | | E(DIHE)=0.000 E(IMPR)=79.898 E(VDW )=-173.835 E(ELEC)=-138.006 | | E(CDIH)=7.125 E(NOE )=131.688 E(PLAN)=18.232 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 62740 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 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 1.42 A apart NBONDS: found 62727 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62712 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62667 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 62639 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.38 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 62638 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62634 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62707 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.37 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62739 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=1137.647 E(kin)=590.383 temperature=292.559 | | Etotal =547.265 grad(E)=65.697 E(BOND)=237.087 E(ANGL)=388.250 | | E(DIHE)=0.000 E(IMPR)=93.387 E(VDW )=-171.199 E(ELEC)=-146.159 | | E(CDIH)=6.978 E(NOE )=123.839 E(PLAN)=15.081 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62781 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.40 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62810 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62829 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62855 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 62904 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62875 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62863 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62867 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62848 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=1146.635 E(kin)=609.095 temperature=301.832 | | Etotal =537.541 grad(E)=62.341 E(BOND)=205.418 E(ANGL)=404.240 | | E(DIHE)=0.000 E(IMPR)=91.386 E(VDW )=-189.387 E(ELEC)=-132.026 | | E(CDIH)=8.137 E(NOE )=138.807 E(PLAN)=10.965 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -H1' " and "A -11 -ADE -N7 " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 62805 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 62769 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62712 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62621 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62576 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62579 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62591 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62571 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62575 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=1125.982 E(kin)=607.794 temperature=301.187 | | Etotal =518.188 grad(E)=62.820 E(BOND)=214.820 E(ANGL)=384.316 | | E(DIHE)=0.000 E(IMPR)=86.556 E(VDW )=-183.261 E(ELEC)=-140.206 | | E(CDIH)=6.924 E(NOE )=130.615 E(PLAN)=18.425 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62521 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62511 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62524 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62479 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62456 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62390 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.22 A apart NBONDS: found 62320 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 62353 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=1154.412 E(kin)=591.489 temperature=293.108 | | Etotal =562.922 grad(E)=64.726 E(BOND)=216.894 E(ANGL)=413.584 | | E(DIHE)=0.000 E(IMPR)=88.203 E(VDW )=-188.251 E(ELEC)=-131.306 | | E(CDIH)=5.949 E(NOE )=139.460 E(PLAN)=18.389 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 62397 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62377 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62412 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62413 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62426 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62440 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62433 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62491 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62480 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=1154.607 E(kin)=636.581 temperature=315.453 | | Etotal =518.025 grad(E)=62.760 E(BOND)=186.618 E(ANGL)=415.529 | | E(DIHE)=0.000 E(IMPR)=90.712 E(VDW )=-182.203 E(ELEC)=-131.681 | | E(CDIH)=4.277 E(NOE )=112.474 E(PLAN)=22.299 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 62541 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62508 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 62536 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 62547 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62538 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 62560 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62567 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62564 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62534 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62501 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=1146.808 E(kin)=618.568 temperature=306.526 | | Etotal =528.241 grad(E)=64.111 E(BOND)=198.920 E(ANGL)=397.641 | | E(DIHE)=0.000 E(IMPR)=95.044 E(VDW )=-195.418 E(ELEC)=-127.960 | | E(CDIH)=6.657 E(NOE )=137.426 E(PLAN)=15.931 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62514 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.21 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 62503 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.24 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62450 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62434 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 62436 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart NBONDS: found 62451 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 62443 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 62457 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 62447 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 62396 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 62429 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62461 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62499 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62496 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 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 1.49 A apart NBONDS: found 62526 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=1152.968 E(kin)=612.564 temperature=303.551 | | Etotal =540.404 grad(E)=65.495 E(BOND)=206.172 E(ANGL)=408.562 | | E(DIHE)=0.000 E(IMPR)=85.609 E(VDW )=-183.547 E(ELEC)=-128.279 | | E(CDIH)=3.720 E(NOE )=135.232 E(PLAN)=12.936 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1145.905 E(kin)=603.430 temperature=299.025 | | Etotal =542.475 grad(E)=65.343 E(BOND)=211.965 E(ANGL)=397.787 | | E(DIHE)=0.000 E(IMPR)=91.644 E(VDW )=-182.793 E(ELEC)=-133.294 | | E(CDIH)=4.998 E(NOE )=135.257 E(PLAN)=16.912 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=38.945 E(kin)=21.670 temperature=10.739 | | Etotal =28.673 grad(E)=2.000 E(BOND)=12.239 E(ANGL)=17.440 | | E(DIHE)=0.000 E(IMPR)=7.187 E(VDW )=7.877 E(ELEC)=7.774 | | E(CDIH)=2.414 E(NOE )=12.793 E(PLAN)=2.815 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62583 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62596 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 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 1.48 A apart NBONDS: found 62673 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62736 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62816 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62892 intra-atom interactions NBONDS: found 63075 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63188 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63323 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=1136.482 E(kin)=606.214 temperature=300.404 | | Etotal =530.268 grad(E)=64.435 E(BOND)=216.774 E(ANGL)=380.932 | | E(DIHE)=0.000 E(IMPR)=96.354 E(VDW )=-195.004 E(ELEC)=-131.285 | | E(CDIH)=6.736 E(NOE )=144.362 E(PLAN)=11.400 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63461 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63524 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 63498 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63529 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63485 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63427 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63370 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=1177.362 E(kin)=603.345 temperature=298.983 | | Etotal =574.017 grad(E)=68.563 E(BOND)=225.849 E(ANGL)=405.361 | | E(DIHE)=0.000 E(IMPR)=98.512 E(VDW )=-169.472 E(ELEC)=-128.602 | | E(CDIH)=8.804 E(NOE )=117.716 E(PLAN)=15.848 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63326 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.23 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63225 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63185 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63171 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 63123 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63033 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63023 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62979 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=1162.427 E(kin)=597.643 temperature=296.157 | | Etotal =564.785 grad(E)=69.418 E(BOND)=205.396 E(ANGL)=407.790 | | E(DIHE)=0.000 E(IMPR)=105.909 E(VDW )=-195.895 E(ELEC)=-128.683 | | E(CDIH)=4.468 E(NOE )=149.245 E(PLAN)=16.556 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63009 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 63047 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62958 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62952 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62941 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62923 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62856 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62944 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63042 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=1168.718 E(kin)=617.422 temperature=305.959 | | Etotal =551.295 grad(E)=67.711 E(BOND)=201.641 E(ANGL)=397.328 | | E(DIHE)=0.000 E(IMPR)=106.897 E(VDW )=-171.917 E(ELEC)=-125.552 | | E(CDIH)=3.362 E(NOE )=124.744 E(PLAN)=14.793 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63079 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63157 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63270 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.22 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63305 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.21 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63372 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63438 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63419 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=1157.800 E(kin)=594.956 temperature=294.826 | | Etotal =562.844 grad(E)=70.464 E(BOND)=205.626 E(ANGL)=379.110 | | E(DIHE)=0.000 E(IMPR)=116.178 E(VDW )=-178.856 E(ELEC)=-138.014 | | E(CDIH)=6.548 E(NOE )=155.236 E(PLAN)=17.017 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63389 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63423 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63443 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63376 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 63389 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 63346 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63339 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 63297 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.50 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 63254 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63218 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=1162.567 E(kin)=603.361 temperature=298.991 | | Etotal =559.206 grad(E)=66.391 E(BOND)=217.214 E(ANGL)=405.458 | | E(DIHE)=0.000 E(IMPR)=92.630 E(VDW )=-174.998 E(ELEC)=-136.042 | | E(CDIH)=5.884 E(NOE )=131.273 E(PLAN)=17.786 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63192 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63208 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63152 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 63154 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63192 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63225 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63251 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63297 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63394 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 63405 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63458 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=1163.433 E(kin)=604.335 temperature=299.474 | | Etotal =559.098 grad(E)=64.701 E(BOND)=216.152 E(ANGL)=405.199 | | E(DIHE)=0.000 E(IMPR)=85.126 E(VDW )=-174.140 E(ELEC)=-147.200 | | E(CDIH)=3.636 E(NOE )=150.017 E(PLAN)=20.308 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63436 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63442 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63421 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63399 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63361 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63330 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63292 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63286 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63189 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63132 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63134 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63108 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=1136.387 E(kin)=633.404 temperature=313.878 | | Etotal =502.982 grad(E)=64.137 E(BOND)=201.427 E(ANGL)=402.014 | | E(DIHE)=0.000 E(IMPR)=86.182 E(VDW )=-195.720 E(ELEC)=-134.349 | | E(CDIH)=5.460 E(NOE )=120.780 E(PLAN)=17.188 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63060 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 63028 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 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 1.45 A apart NBONDS: found 62981 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63006 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62988 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.50 A apart NBONDS: found 62936 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62882 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart NBONDS: found 62835 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62822 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62731 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=1171.073 E(kin)=593.411 temperature=294.060 | | Etotal =577.662 grad(E)=66.605 E(BOND)=243.975 E(ANGL)=399.482 | | E(DIHE)=0.000 E(IMPR)=95.236 E(VDW )=-180.444 E(ELEC)=-128.734 | | E(CDIH)=5.730 E(NOE )=128.942 E(PLAN)=13.476 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.35 A apart NBONDS: found 62609 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 62566 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 62533 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart NBONDS: found 62520 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62478 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62455 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62432 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62490 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62548 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=1142.553 E(kin)=611.524 temperature=303.036 | | Etotal =531.029 grad(E)=63.891 E(BOND)=204.763 E(ANGL)=393.145 | | E(DIHE)=0.000 E(IMPR)=85.848 E(VDW )=-174.042 E(ELEC)=-128.986 | | E(CDIH)=6.249 E(NOE )=126.567 E(PLAN)=17.485 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1156.447 E(kin)=605.530 temperature=300.065 | | Etotal =550.917 grad(E)=66.720 E(BOND)=214.788 E(ANGL)=401.486 | | E(DIHE)=0.000 E(IMPR)=96.977 E(VDW )=-183.267 E(ELEC)=-132.003 | | E(CDIH)=4.775 E(NOE )=131.760 E(PLAN)=16.402 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.396 E(kin)=12.273 temperature=6.082 | | Etotal =16.494 grad(E)=1.599 E(BOND)=9.977 E(ANGL)=13.196 | | E(DIHE)=0.000 E(IMPR)=7.832 E(VDW )=8.448 E(ELEC)=5.876 | | E(CDIH)=2.043 E(NOE )=11.674 E(PLAN)=2.078 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=1151.176 E(kin)=604.480 temperature=299.545 | | Etotal =546.696 grad(E)=66.031 E(BOND)=213.376 E(ANGL)=399.636 | | E(DIHE)=0.000 E(IMPR)=94.311 E(VDW )=-183.030 E(ELEC)=-132.649 | | E(CDIH)=4.886 E(NOE )=133.508 E(PLAN)=16.657 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=29.173 E(kin)=17.642 temperature=8.742 | | Etotal =23.768 grad(E)=1.937 E(BOND)=11.254 E(ANGL)=15.575 | | E(DIHE)=0.000 E(IMPR)=7.976 E(VDW )=8.171 E(ELEC)=6.921 | | E(CDIH)=2.239 E(NOE )=12.371 E(PLAN)=2.487 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62590 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 62682 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart NBONDS: found 62755 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 62736 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 62736 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 62736 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 62733 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 62722 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=1137.124 E(kin)=600.489 temperature=297.568 | | Etotal =536.635 grad(E)=67.375 E(BOND)=210.321 E(ANGL)=386.380 | | E(DIHE)=0.000 E(IMPR)=93.107 E(VDW )=-185.840 E(ELEC)=-130.912 | | E(CDIH)=5.354 E(NOE )=140.137 E(PLAN)=18.087 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 62671 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 62638 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 62613 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 62605 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 62572 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62619 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62619 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62745 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62796 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=1162.736 E(kin)=592.893 temperature=293.804 | | Etotal =569.843 grad(E)=69.132 E(BOND)=226.915 E(ANGL)=399.792 | | E(DIHE)=0.000 E(IMPR)=102.838 E(VDW )=-185.724 E(ELEC)=-125.217 | | E(CDIH)=5.632 E(NOE )=130.522 E(PLAN)=15.086 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62828 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62842 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 62810 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62856 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62835 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart NBONDS: found 62855 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62829 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62794 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=1152.387 E(kin)=621.336 temperature=307.898 | | Etotal =531.051 grad(E)=67.316 E(BOND)=207.502 E(ANGL)=393.963 | | E(DIHE)=0.000 E(IMPR)=95.788 E(VDW )=-200.614 E(ELEC)=-128.715 | | E(CDIH)=3.978 E(NOE )=146.038 E(PLAN)=13.110 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62738 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 62711 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 62608 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 62564 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62534 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 62490 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62483 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 62483 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62425 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=1159.892 E(kin)=598.833 temperature=296.747 | | Etotal =561.058 grad(E)=66.779 E(BOND)=239.705 E(ANGL)=401.518 | | E(DIHE)=0.000 E(IMPR)=90.888 E(VDW )=-185.068 E(ELEC)=-134.446 | | E(CDIH)=3.277 E(NOE )=129.147 E(PLAN)=16.036 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 62436 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 62459 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart NBONDS: found 62470 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 62589 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 62626 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 62614 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62628 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62666 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.43 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 62643 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=1148.629 E(kin)=606.170 temperature=300.382 | | Etotal =542.459 grad(E)=64.848 E(BOND)=227.382 E(ANGL)=405.060 | | E(DIHE)=0.000 E(IMPR)=77.187 E(VDW )=-184.404 E(ELEC)=-138.287 | | E(CDIH)=2.424 E(NOE )=136.531 E(PLAN)=16.566 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 62642 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 62584 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62566 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62505 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62452 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62401 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62281 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 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 1.47 A apart NBONDS: found 62208 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=1154.945 E(kin)=615.785 temperature=305.147 | | Etotal =539.160 grad(E)=66.112 E(BOND)=214.795 E(ANGL)=381.193 | | E(DIHE)=0.000 E(IMPR)=89.371 E(VDW )=-186.379 E(ELEC)=-125.480 | | E(CDIH)=6.700 E(NOE )=142.143 E(PLAN)=16.818 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 62167 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 62183 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62208 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62219 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 62219 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 62170 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 62181 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 62160 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62156 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62128 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62057 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=1156.560 E(kin)=583.693 temperature=289.244 | | Etotal =572.867 grad(E)=67.238 E(BOND)=209.036 E(ANGL)=413.012 | | E(DIHE)=0.000 E(IMPR)=108.847 E(VDW )=-180.721 E(ELEC)=-136.062 | | E(CDIH)=7.082 E(NOE )=134.553 E(PLAN)=17.119 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62024 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62007 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61984 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 61996 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 62067 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 61984 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 62003 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62038 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=1154.101 E(kin)=591.104 temperature=292.917 | | Etotal =562.996 grad(E)=68.224 E(BOND)=218.440 E(ANGL)=406.253 | | E(DIHE)=0.000 E(IMPR)=91.740 E(VDW )=-185.476 E(ELEC)=-130.553 | | E(CDIH)=6.059 E(NOE )=138.716 E(PLAN)=17.818 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62074 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62136 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62152 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62146 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62174 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62174 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62174 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62129 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=1185.566 E(kin)=608.678 temperature=301.625 | | Etotal =576.888 grad(E)=68.364 E(BOND)=234.114 E(ANGL)=420.599 | | E(DIHE)=0.000 E(IMPR)=92.119 E(VDW )=-187.737 E(ELEC)=-123.276 | | E(CDIH)=8.959 E(NOE )=116.575 E(PLAN)=15.535 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62194 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62216 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62230 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62299 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62356 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62435 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62517 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62607 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62658 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62723 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=1145.076 E(kin)=616.980 temperature=305.739 | | Etotal =528.096 grad(E)=64.631 E(BOND)=215.178 E(ANGL)=385.465 | | E(DIHE)=0.000 E(IMPR)=89.997 E(VDW )=-177.515 E(ELEC)=-133.964 | | E(CDIH)=3.480 E(NOE )=130.321 E(PLAN)=15.134 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1154.993 E(kin)=605.472 temperature=300.037 | | Etotal =549.521 grad(E)=66.658 E(BOND)=216.433 E(ANGL)=401.155 | | E(DIHE)=0.000 E(IMPR)=94.547 E(VDW )=-183.825 E(ELEC)=-130.690 | | E(CDIH)=5.138 E(NOE )=130.494 E(PLAN)=16.268 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.126 E(kin)=12.157 temperature=6.024 | | Etotal =16.842 grad(E)=1.681 E(BOND)=9.686 E(ANGL)=14.088 | | E(DIHE)=0.000 E(IMPR)=7.031 E(VDW )=8.032 E(ELEC)=5.427 | | E(CDIH)=2.166 E(NOE )=9.589 E(PLAN)=1.933 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=1152.448 E(kin)=604.810 temperature=299.709 | | Etotal =547.638 grad(E)=66.240 E(BOND)=214.395 E(ANGL)=400.143 | | E(DIHE)=0.000 E(IMPR)=94.390 E(VDW )=-183.295 E(ELEC)=-131.996 | | E(CDIH)=4.970 E(NOE )=132.504 E(PLAN)=16.527 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=24.892 E(kin)=16.030 temperature=7.944 | | Etotal =21.747 grad(E)=1.879 E(BOND)=10.853 E(ANGL)=15.112 | | E(DIHE)=0.000 E(IMPR)=7.674 E(VDW )=8.133 E(ELEC)=6.527 | | E(CDIH)=2.218 E(NOE )=11.606 E(PLAN)=2.325 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62782 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62776 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62787 intra-atom interactions %atoms "A -1 -GUA -O5T " and "A -1 -GUA -H8 " only 1.47 A apart %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62799 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62851 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 62904 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62942 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=1174.177 E(kin)=613.266 temperature=303.899 | | Etotal =560.912 grad(E)=66.003 E(BOND)=209.547 E(ANGL)=409.888 | | E(DIHE)=0.000 E(IMPR)=96.241 E(VDW )=-178.862 E(ELEC)=-135.190 | | E(CDIH)=6.690 E(NOE )=134.603 E(PLAN)=17.995 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62937 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62891 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62845 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62835 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62877 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 62942 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63002 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=1145.622 E(kin)=619.758 temperature=307.116 | | Etotal =525.864 grad(E)=69.050 E(BOND)=210.963 E(ANGL)=393.271 | | E(DIHE)=0.000 E(IMPR)=92.950 E(VDW )=-175.482 E(ELEC)=-141.727 | | E(CDIH)=9.223 E(NOE )=118.100 E(PLAN)=18.566 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 63074 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 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 1.41 A apart NBONDS: found 63137 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63174 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63175 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 63179 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 63106 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 63066 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=1160.099 E(kin)=633.247 temperature=313.800 | | Etotal =526.852 grad(E)=66.592 E(BOND)=205.146 E(ANGL)=387.053 | | E(DIHE)=0.000 E(IMPR)=94.239 E(VDW )=-179.582 E(ELEC)=-136.123 | | E(CDIH)=2.837 E(NOE )=140.128 E(PLAN)=13.156 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62992 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 62995 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 62895 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart NBONDS: found 62787 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.47 A apart %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62754 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.49 A apart %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 62744 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart NBONDS: found 62735 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62765 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62804 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=1143.935 E(kin)=614.999 temperature=304.758 | | Etotal =528.936 grad(E)=65.650 E(BOND)=200.322 E(ANGL)=409.866 | | E(DIHE)=0.000 E(IMPR)=93.558 E(VDW )=-181.551 E(ELEC)=-131.510 | | E(CDIH)=4.430 E(NOE )=119.030 E(PLAN)=14.791 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62913 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.36 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62966 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63036 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63054 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 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 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62977 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62881 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62884 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.49 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 62838 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 62740 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=1143.916 E(kin)=604.671 temperature=299.640 | | Etotal =539.244 grad(E)=65.762 E(BOND)=216.599 E(ANGL)=398.698 | | E(DIHE)=0.000 E(IMPR)=90.919 E(VDW )=-176.970 E(ELEC)=-147.730 | | E(CDIH)=7.187 E(NOE )=132.819 E(PLAN)=17.720 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62644 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 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 1.47 A apart NBONDS: found 62562 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62487 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62322 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 62259 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 62219 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart NBONDS: found 62222 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 62282 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=1128.330 E(kin)=612.333 temperature=303.437 | | Etotal =515.997 grad(E)=65.000 E(BOND)=221.370 E(ANGL)=393.763 | | E(DIHE)=0.000 E(IMPR)=86.904 E(VDW )=-199.876 E(ELEC)=-141.576 | | E(CDIH)=3.046 E(NOE )=134.925 E(PLAN)=17.442 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 62327 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart NBONDS: found 62462 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart NBONDS: found 62547 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart NBONDS: found 62627 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 62696 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62723 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 62760 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62752 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=1159.643 E(kin)=605.057 temperature=299.831 | | Etotal =554.586 grad(E)=67.978 E(BOND)=210.935 E(ANGL)=427.815 | | E(DIHE)=0.000 E(IMPR)=95.709 E(VDW )=-182.963 E(ELEC)=-143.028 | | E(CDIH)=5.674 E(NOE )=125.997 E(PLAN)=14.445 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.23 A apart NBONDS: found 62787 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart NBONDS: found 62802 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 62840 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart NBONDS: found 62840 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62853 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 62831 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62863 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62880 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=1137.125 E(kin)=590.493 temperature=292.614 | | Etotal =546.633 grad(E)=68.807 E(BOND)=199.799 E(ANGL)=419.556 | | E(DIHE)=0.000 E(IMPR)=90.613 E(VDW )=-173.480 E(ELEC)=-136.306 | | E(CDIH)=2.646 E(NOE )=127.721 E(PLAN)=16.083 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart NBONDS: found 62947 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63038 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63087 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63127 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63233 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart NBONDS: found 63301 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart NBONDS: found 63367 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63457 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=1130.806 E(kin)=599.657 temperature=297.155 | | Etotal =531.150 grad(E)=66.930 E(BOND)=221.309 E(ANGL)=420.243 | | E(DIHE)=0.000 E(IMPR)=78.815 E(VDW )=-203.092 E(ELEC)=-139.550 | | E(CDIH)=2.294 E(NOE )=134.080 E(PLAN)=17.051 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63515 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63584 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63605 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63634 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63672 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63720 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63766 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63767 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=1145.729 E(kin)=628.082 temperature=311.241 | | Etotal =517.648 grad(E)=66.336 E(BOND)=212.515 E(ANGL)=420.175 | | E(DIHE)=0.000 E(IMPR)=80.020 E(VDW )=-195.969 E(ELEC)=-145.771 | | E(CDIH)=3.579 E(NOE )=125.906 E(PLAN)=17.192 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1149.101 E(kin)=605.504 temperature=300.053 | | Etotal =543.598 grad(E)=66.968 E(BOND)=214.151 E(ANGL)=404.886 | | E(DIHE)=0.000 E(IMPR)=95.085 E(VDW )=-184.435 E(ELEC)=-139.385 | | E(CDIH)=5.170 E(NOE )=132.019 E(PLAN)=16.105 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.664 E(kin)=12.673 temperature=6.280 | | Etotal =17.641 grad(E)=1.691 E(BOND)=10.890 E(ANGL)=14.879 | | E(DIHE)=0.000 E(IMPR)=7.531 E(VDW )=9.132 E(ELEC)=5.011 | | E(CDIH)=2.190 E(NOE )=10.056 E(PLAN)=1.757 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=1151.612 E(kin)=604.984 temperature=299.795 | | Etotal =546.628 grad(E)=66.422 E(BOND)=214.334 E(ANGL)=401.329 | | E(DIHE)=0.000 E(IMPR)=94.563 E(VDW )=-183.580 E(ELEC)=-133.843 | | E(CDIH)=5.020 E(NOE )=132.383 E(PLAN)=16.422 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=22.515 E(kin)=15.263 temperature=7.564 | | Etotal =20.870 grad(E)=1.861 E(BOND)=10.863 E(ANGL)=15.194 | | E(DIHE)=0.000 E(IMPR)=7.645 E(VDW )=8.409 E(ELEC)=6.962 | | E(CDIH)=2.213 E(NOE )=11.240 E(PLAN)=2.204 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63759 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63695 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63623 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63604 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 63597 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 63613 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart NBONDS: found 63646 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63684 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=1153.923 E(kin)=627.108 temperature=310.758 | | Etotal =526.815 grad(E)=67.582 E(BOND)=214.925 E(ANGL)=384.624 | | E(DIHE)=0.000 E(IMPR)=100.851 E(VDW )=-193.912 E(ELEC)=-139.582 | | E(CDIH)=6.301 E(NOE )=135.276 E(PLAN)=18.332 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63848 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63911 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63954 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64052 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64180 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64226 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64253 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64232 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=1154.535 E(kin)=610.692 temperature=302.623 | | Etotal =543.843 grad(E)=67.866 E(BOND)=221.676 E(ANGL)=407.442 | | E(DIHE)=0.000 E(IMPR)=96.750 E(VDW )=-184.511 E(ELEC)=-146.242 | | E(CDIH)=4.336 E(NOE )=129.065 E(PLAN)=15.327 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64179 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64145 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 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 1.45 A apart NBONDS: found 64084 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64024 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64061 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64042 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63970 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63969 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=1137.354 E(kin)=599.006 temperature=296.832 | | Etotal =538.348 grad(E)=68.707 E(BOND)=224.805 E(ANGL)=404.689 | | E(DIHE)=0.000 E(IMPR)=93.706 E(VDW )=-189.731 E(ELEC)=-139.358 | | E(CDIH)=5.879 E(NOE )=127.307 E(PLAN)=11.051 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63961 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63898 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63830 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63776 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63744 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63739 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63691 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63661 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=1139.923 E(kin)=605.858 temperature=300.228 | | Etotal =534.065 grad(E)=66.719 E(BOND)=241.693 E(ANGL)=410.209 | | E(DIHE)=0.000 E(IMPR)=90.463 E(VDW )=-186.344 E(ELEC)=-145.302 | | E(CDIH)=6.133 E(NOE )=104.864 E(PLAN)=12.348 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63593 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63617 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63601 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63570 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63491 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63484 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63411 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63353 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=1147.894 E(kin)=585.023 temperature=289.904 | | Etotal =562.871 grad(E)=68.674 E(BOND)=220.447 E(ANGL)=412.563 | | E(DIHE)=0.000 E(IMPR)=108.551 E(VDW )=-183.855 E(ELEC)=-146.264 | | E(CDIH)=6.268 E(NOE )=127.981 E(PLAN)=17.180 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63260 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 63179 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63069 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63066 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63069 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63050 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 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 1.47 A apart NBONDS: found 63010 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63083 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=1156.674 E(kin)=605.046 temperature=299.826 | | Etotal =551.628 grad(E)=68.157 E(BOND)=213.819 E(ANGL)=411.758 | | E(DIHE)=0.000 E(IMPR)=98.033 E(VDW )=-178.244 E(ELEC)=-151.420 | | E(CDIH)=3.144 E(NOE )=134.007 E(PLAN)=20.532 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63130 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63113 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63002 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62890 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H4' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62771 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62660 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62526 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=1159.831 E(kin)=600.972 temperature=297.807 | | Etotal =558.859 grad(E)=68.404 E(BOND)=225.487 E(ANGL)=409.811 | | E(DIHE)=0.000 E(IMPR)=86.652 E(VDW )=-177.130 E(ELEC)=-147.585 | | E(CDIH)=5.959 E(NOE )=142.275 E(PLAN)=13.389 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62378 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 62270 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 62191 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62258 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62401 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=1153.931 E(kin)=604.066 temperature=299.340 | | Etotal =549.865 grad(E)=68.217 E(BOND)=226.850 E(ANGL)=399.392 | | E(DIHE)=0.000 E(IMPR)=96.604 E(VDW )=-181.381 E(ELEC)=-142.342 | | E(CDIH)=4.060 E(NOE )=131.114 E(PLAN)=15.567 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62410 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62489 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62491 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 62514 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62446 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62391 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=1170.299 E(kin)=612.501 temperature=303.520 | | Etotal =557.799 grad(E)=69.170 E(BOND)=224.129 E(ANGL)=390.213 | | E(DIHE)=0.000 E(IMPR)=108.697 E(VDW )=-189.835 E(ELEC)=-131.571 | | E(CDIH)=4.222 E(NOE )=136.478 E(PLAN)=15.466 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62370 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62375 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62405 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62520 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62569 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62546 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62609 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=1172.285 E(kin)=621.857 temperature=308.156 | | Etotal =550.427 grad(E)=68.027 E(BOND)=224.167 E(ANGL)=429.460 | | E(DIHE)=0.000 E(IMPR)=97.887 E(VDW )=-179.179 E(ELEC)=-147.725 | | E(CDIH)=4.364 E(NOE )=101.727 E(PLAN)=19.727 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1149.972 E(kin)=605.389 temperature=299.996 | | Etotal =544.582 grad(E)=68.430 E(BOND)=222.038 E(ANGL)=404.207 | | E(DIHE)=0.000 E(IMPR)=97.299 E(VDW )=-186.668 E(ELEC)=-143.442 | | E(CDIH)=5.675 E(NOE )=129.910 E(PLAN)=15.562 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.954 E(kin)=12.415 temperature=6.152 | | Etotal =17.018 grad(E)=1.718 E(BOND)=10.000 E(ANGL)=14.322 | | E(DIHE)=0.000 E(IMPR)=7.325 E(VDW )=8.017 E(ELEC)=5.364 | | E(CDIH)=2.338 E(NOE )=10.367 E(PLAN)=2.152 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=1151.284 E(kin)=605.065 temperature=299.835 | | Etotal =546.219 grad(E)=66.824 E(BOND)=215.875 E(ANGL)=401.904 | | E(DIHE)=0.000 E(IMPR)=95.111 E(VDW )=-184.197 E(ELEC)=-135.763 | | E(CDIH)=5.151 E(NOE )=131.888 E(PLAN)=16.250 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=20.846 E(kin)=14.739 temperature=7.304 | | Etotal =20.175 grad(E)=2.001 E(BOND)=11.131 E(ANGL)=15.068 | | E(DIHE)=0.000 E(IMPR)=7.660 E(VDW )=8.423 E(ELEC)=7.698 | | E(CDIH)=2.253 E(NOE )=11.115 E(PLAN)=2.221 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62634 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 62653 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 62701 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62719 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62602 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62677 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=1165.458 E(kin)=614.569 temperature=304.545 | | Etotal =550.889 grad(E)=69.374 E(BOND)=216.415 E(ANGL)=380.491 | | E(DIHE)=0.000 E(IMPR)=114.509 E(VDW )=-187.647 E(ELEC)=-135.481 | | E(CDIH)=11.752 E(NOE )=135.637 E(PLAN)=15.213 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62725 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62783 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 62851 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62995 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63127 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63191 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63224 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63282 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=1149.775 E(kin)=617.483 temperature=305.989 | | Etotal =532.293 grad(E)=67.309 E(BOND)=236.029 E(ANGL)=373.638 | | E(DIHE)=0.000 E(IMPR)=98.644 E(VDW )=-176.434 E(ELEC)=-141.337 | | E(CDIH)=7.467 E(NOE )=119.059 E(PLAN)=15.227 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63343 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63378 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 63360 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 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 1.40 A apart NBONDS: found 63448 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63459 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63375 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 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 1.40 A apart NBONDS: found 63308 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=1193.835 E(kin)=618.765 temperature=306.624 | | Etotal =575.070 grad(E)=70.667 E(BOND)=234.338 E(ANGL)=404.624 | | E(DIHE)=0.000 E(IMPR)=93.337 E(VDW )=-184.140 E(ELEC)=-130.411 | | E(CDIH)=1.861 E(NOE )=141.573 E(PLAN)=13.887 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63267 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63249 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63270 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63286 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63215 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63171 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.40 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63157 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=1145.888 E(kin)=612.951 temperature=303.743 | | Etotal =532.936 grad(E)=71.033 E(BOND)=226.143 E(ANGL)=396.372 | | E(DIHE)=0.000 E(IMPR)=88.256 E(VDW )=-193.470 E(ELEC)=-140.969 | | E(CDIH)=4.768 E(NOE )=133.423 E(PLAN)=18.413 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63084 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.36 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 63002 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62900 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62847 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 62770 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62652 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 62622 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 62606 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=1154.608 E(kin)=611.490 temperature=303.019 | | Etotal =543.118 grad(E)=66.556 E(BOND)=237.663 E(ANGL)=393.641 | | E(DIHE)=0.000 E(IMPR)=87.301 E(VDW )=-192.794 E(ELEC)=-137.332 | | E(CDIH)=3.196 E(NOE )=135.950 E(PLAN)=15.493 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 62659 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62727 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62780 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 62759 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62715 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62660 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62698 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=1145.658 E(kin)=587.272 temperature=291.018 | | Etotal =558.386 grad(E)=72.771 E(BOND)=237.789 E(ANGL)=408.200 | | E(DIHE)=0.000 E(IMPR)=95.476 E(VDW )=-181.198 E(ELEC)=-140.657 | | E(CDIH)=3.365 E(NOE )=120.627 E(PLAN)=14.785 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 62704 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62730 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 62871 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 62915 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart NBONDS: found 62966 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63066 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63051 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=1174.337 E(kin)=602.845 temperature=298.735 | | Etotal =571.492 grad(E)=68.159 E(BOND)=236.922 E(ANGL)=401.582 | | E(DIHE)=0.000 E(IMPR)=102.668 E(VDW )=-203.511 E(ELEC)=-132.366 | | E(CDIH)=3.363 E(NOE )=149.523 E(PLAN)=13.311 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 63027 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63002 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63042 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 62996 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 62991 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63025 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 63009 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=1139.189 E(kin)=616.374 temperature=305.439 | | Etotal =522.816 grad(E)=67.603 E(BOND)=208.469 E(ANGL)=396.052 | | E(DIHE)=0.000 E(IMPR)=100.719 E(VDW )=-192.327 E(ELEC)=-132.408 | | E(CDIH)=7.621 E(NOE )=120.182 E(PLAN)=14.509 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63105 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63187 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63315 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63375 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63470 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63593 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63656 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63713 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=1140.575 E(kin)=606.252 temperature=300.423 | | Etotal =534.322 grad(E)=67.826 E(BOND)=216.032 E(ANGL)=391.438 | | E(DIHE)=0.000 E(IMPR)=111.452 E(VDW )=-190.098 E(ELEC)=-144.692 | | E(CDIH)=4.114 E(NOE )=131.420 E(PLAN)=14.658 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart NBONDS: found 63668 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63703 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart NBONDS: found 63699 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 63680 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63688 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 63661 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 63749 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=1156.717 E(kin)=595.873 temperature=295.280 | | Etotal =560.844 grad(E)=68.660 E(BOND)=238.092 E(ANGL)=404.222 | | E(DIHE)=0.000 E(IMPR)=103.564 E(VDW )=-188.737 E(ELEC)=-138.446 | | E(CDIH)=3.620 E(NOE )=122.265 E(PLAN)=16.265 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1152.542 E(kin)=605.538 temperature=300.070 | | Etotal =547.003 grad(E)=68.993 E(BOND)=227.423 E(ANGL)=402.168 | | E(DIHE)=0.000 E(IMPR)=95.020 E(VDW )=-187.752 E(ELEC)=-139.144 | | E(CDIH)=5.053 E(NOE )=128.007 E(PLAN)=16.229 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.559 E(kin)=12.278 temperature=6.084 | | Etotal =17.295 grad(E)=1.847 E(BOND)=10.084 E(ANGL)=12.528 | | E(DIHE)=0.000 E(IMPR)=7.809 E(VDW )=8.282 E(ELEC)=5.088 | | E(CDIH)=2.221 E(NOE )=10.852 E(PLAN)=1.997 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=1151.493 E(kin)=605.144 temperature=299.874 | | Etotal =546.350 grad(E)=67.185 E(BOND)=217.800 E(ANGL)=401.948 | | E(DIHE)=0.000 E(IMPR)=95.096 E(VDW )=-184.790 E(ELEC)=-136.326 | | E(CDIH)=5.135 E(NOE )=131.241 E(PLAN)=16.246 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=19.714 E(kin)=14.359 temperature=7.116 | | Etotal =19.727 grad(E)=2.135 E(BOND)=11.778 E(ANGL)=14.675 | | E(DIHE)=0.000 E(IMPR)=7.685 E(VDW )=8.503 E(ELEC)=7.436 | | E(CDIH)=2.248 E(NOE )=11.166 E(PLAN)=2.185 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63793 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63853 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63909 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63927 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64021 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64127 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64144 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64246 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=1152.335 E(kin)=602.028 temperature=298.330 | | Etotal =550.307 grad(E)=69.359 E(BOND)=224.374 E(ANGL)=397.257 | | E(DIHE)=0.000 E(IMPR)=107.429 E(VDW )=-187.013 E(ELEC)=-146.623 | | E(CDIH)=3.954 E(NOE )=140.713 E(PLAN)=10.217 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64279 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 64359 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64434 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64475 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64437 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64421 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart NBONDS: found 64375 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 64298 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=1151.701 E(kin)=603.489 temperature=299.054 | | Etotal =548.212 grad(E)=69.238 E(BOND)=228.090 E(ANGL)=414.272 | | E(DIHE)=0.000 E(IMPR)=96.586 E(VDW )=-189.815 E(ELEC)=-143.952 | | E(CDIH)=7.344 E(NOE )=123.929 E(PLAN)=11.756 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 64241 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart NBONDS: found 64184 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart NBONDS: found 64180 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 64135 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 64130 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart NBONDS: found 64092 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart NBONDS: found 64095 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart NBONDS: found 64096 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 64042 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=1158.833 E(kin)=622.497 temperature=308.473 | | Etotal =536.335 grad(E)=68.194 E(BOND)=222.325 E(ANGL)=400.473 | | E(DIHE)=0.000 E(IMPR)=99.998 E(VDW )=-198.951 E(ELEC)=-138.726 | | E(CDIH)=1.013 E(NOE )=135.263 E(PLAN)=14.940 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 64037 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63971 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63862 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63785 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63741 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63665 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63603 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63512 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 63479 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=1148.569 E(kin)=600.651 temperature=297.648 | | Etotal =547.918 grad(E)=67.909 E(BOND)=214.865 E(ANGL)=421.302 | | E(DIHE)=0.000 E(IMPR)=90.148 E(VDW )=-192.353 E(ELEC)=-143.311 | | E(CDIH)=5.114 E(NOE )=131.130 E(PLAN)=21.023 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63416 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart NBONDS: found 63364 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63380 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63399 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63451 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63503 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63541 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63658 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63776 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=1147.548 E(kin)=623.893 temperature=309.165 | | Etotal =523.656 grad(E)=67.874 E(BOND)=224.016 E(ANGL)=378.529 | | E(DIHE)=0.000 E(IMPR)=101.735 E(VDW )=-202.367 E(ELEC)=-143.464 | | E(CDIH)=5.198 E(NOE )=144.295 E(PLAN)=15.714 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63795 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63810 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63921 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 64025 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63988 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.42 A apart NBONDS: found 64018 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 63997 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63984 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=1153.844 E(kin)=589.547 temperature=292.145 | | Etotal =564.297 grad(E)=71.639 E(BOND)=242.358 E(ANGL)=392.625 | | E(DIHE)=0.000 E(IMPR)=107.078 E(VDW )=-172.382 E(ELEC)=-141.818 | | E(CDIH)=4.676 E(NOE )=118.256 E(PLAN)=13.502 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63950 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart NBONDS: found 63960 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 63958 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63936 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63975 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart NBONDS: found 63971 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart NBONDS: found 63929 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63875 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=1143.566 E(kin)=591.674 temperature=293.199 | | Etotal =551.892 grad(E)=68.677 E(BOND)=229.430 E(ANGL)=415.701 | | E(DIHE)=0.000 E(IMPR)=96.362 E(VDW )=-193.158 E(ELEC)=-146.299 | | E(CDIH)=4.320 E(NOE )=134.636 E(PLAN)=10.899 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63794 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63733 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart NBONDS: found 63649 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63535 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63568 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63566 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63520 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63493 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=1136.079 E(kin)=620.456 temperature=307.462 | | Etotal =515.623 grad(E)=70.059 E(BOND)=222.091 E(ANGL)=388.641 | | E(DIHE)=0.000 E(IMPR)=97.112 E(VDW )=-183.146 E(ELEC)=-147.806 | | E(CDIH)=4.375 E(NOE )=119.321 E(PLAN)=15.036 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63492 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63425 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63364 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63336 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63314 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63299 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63339 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart NBONDS: found 63359 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=1154.755 E(kin)=590.824 temperature=292.778 | | Etotal =563.931 grad(E)=71.636 E(BOND)=213.859 E(ANGL)=441.656 | | E(DIHE)=0.000 E(IMPR)=97.290 E(VDW )=-194.067 E(ELEC)=-141.540 | | E(CDIH)=3.793 E(NOE )=120.834 E(PLAN)=22.107 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63385 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63411 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63455 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63502 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63469 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63508 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63497 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63479 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63482 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=1149.093 E(kin)=593.800 temperature=294.253 | | Etotal =555.293 grad(E)=68.758 E(BOND)=223.803 E(ANGL)=404.682 | | E(DIHE)=0.000 E(IMPR)=101.891 E(VDW )=-175.875 E(ELEC)=-137.920 | | E(CDIH)=3.849 E(NOE )=116.792 E(PLAN)=18.071 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1147.629 E(kin)=605.543 temperature=300.072 | | Etotal =542.086 grad(E)=69.399 E(BOND)=223.018 E(ANGL)=404.381 | | E(DIHE)=0.000 E(IMPR)=100.262 E(VDW )=-189.601 E(ELEC)=-143.925 | | E(CDIH)=4.493 E(NOE )=127.417 E(PLAN)=16.041 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.398 E(kin)=13.240 temperature=6.561 | | Etotal =15.954 grad(E)=1.919 E(BOND)=10.378 E(ANGL)=12.327 | | E(DIHE)=0.000 E(IMPR)=7.724 E(VDW )=7.160 E(ELEC)=3.883 | | E(CDIH)=1.776 E(NOE )=10.126 E(PLAN)=2.956 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=1150.941 E(kin)=605.201 temperature=299.902 | | Etotal =545.740 grad(E)=67.501 E(BOND)=218.545 E(ANGL)=402.296 | | E(DIHE)=0.000 E(IMPR)=95.834 E(VDW )=-185.477 E(ELEC)=-137.412 | | E(CDIH)=5.043 E(NOE )=130.695 E(PLAN)=16.217 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=18.643 E(kin)=14.205 temperature=7.039 | | Etotal =19.291 grad(E)=2.244 E(BOND)=11.731 E(ANGL)=14.389 | | E(DIHE)=0.000 E(IMPR)=7.901 E(VDW )=8.493 E(ELEC)=7.524 | | E(CDIH)=2.199 E(NOE )=11.104 E(PLAN)=2.312 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63491 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63491 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63468 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63384 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63369 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63420 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63414 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63496 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=1142.856 E(kin)=604.847 temperature=299.727 | | Etotal =538.009 grad(E)=70.180 E(BOND)=217.257 E(ANGL)=410.476 | | E(DIHE)=0.000 E(IMPR)=105.253 E(VDW )=-189.041 E(ELEC)=-139.119 | | E(CDIH)=4.905 E(NOE )=114.355 E(PLAN)=13.923 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63550 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63561 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63579 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63636 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 63593 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 63531 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 63504 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=1135.129 E(kin)=583.220 temperature=289.010 | | Etotal =551.909 grad(E)=70.188 E(BOND)=223.480 E(ANGL)=420.139 | | E(DIHE)=0.000 E(IMPR)=109.068 E(VDW )=-172.228 E(ELEC)=-146.771 | | E(CDIH)=2.816 E(NOE )=104.323 E(PLAN)=11.081 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63509 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63460 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 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 1.39 A apart NBONDS: found 63427 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63390 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 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 1.40 A apart NBONDS: found 63327 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63200 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 63155 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63056 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=1165.490 E(kin)=616.689 temperature=305.595 | | Etotal =548.801 grad(E)=70.700 E(BOND)=203.061 E(ANGL)=401.453 | | E(DIHE)=0.000 E(IMPR)=116.462 E(VDW )=-204.839 E(ELEC)=-135.535 | | E(CDIH)=5.219 E(NOE )=146.055 E(PLAN)=16.925 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 62963 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62940 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62930 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart NBONDS: found 62899 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 62930 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62956 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 62929 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart NBONDS: found 62962 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 63006 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 63073 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=1151.298 E(kin)=598.461 temperature=296.563 | | Etotal =552.837 grad(E)=69.910 E(BOND)=222.246 E(ANGL)=398.311 | | E(DIHE)=0.000 E(IMPR)=102.205 E(VDW )=-178.591 E(ELEC)=-138.409 | | E(CDIH)=5.349 E(NOE )=124.811 E(PLAN)=16.916 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63147 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart NBONDS: found 63203 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63215 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63255 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63282 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 63297 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63324 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 63353 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63361 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 63414 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=1155.079 E(kin)=629.872 temperature=312.128 | | Etotal =525.207 grad(E)=69.486 E(BOND)=207.998 E(ANGL)=391.202 | | E(DIHE)=0.000 E(IMPR)=105.724 E(VDW )=-189.984 E(ELEC)=-139.711 | | E(CDIH)=10.015 E(NOE )=126.370 E(PLAN)=13.593 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63417 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63412 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63428 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63371 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63367 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 63351 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 63361 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=1151.837 E(kin)=609.915 temperature=302.239 | | Etotal =541.921 grad(E)=71.766 E(BOND)=218.343 E(ANGL)=412.314 | | E(DIHE)=0.000 E(IMPR)=91.622 E(VDW )=-193.261 E(ELEC)=-139.652 | | E(CDIH)=4.327 E(NOE )=134.230 E(PLAN)=13.999 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 63359 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63423 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 63453 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63524 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63559 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63636 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.34 A apart NBONDS: found 63660 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63673 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart NBONDS: found 63674 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=1143.670 E(kin)=597.169 temperature=295.922 | | Etotal =546.501 grad(E)=67.426 E(BOND)=218.758 E(ANGL)=415.014 | | E(DIHE)=0.000 E(IMPR)=97.517 E(VDW )=-189.340 E(ELEC)=-132.398 | | E(CDIH)=3.542 E(NOE )=118.755 E(PLAN)=14.654 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63664 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 63762 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63846 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 63908 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63923 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64000 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 64062 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 63992 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63936 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=1148.880 E(kin)=596.622 temperature=295.651 | | Etotal =552.258 grad(E)=73.102 E(BOND)=222.679 E(ANGL)=422.988 | | E(DIHE)=0.000 E(IMPR)=107.221 E(VDW )=-188.816 E(ELEC)=-140.986 | | E(CDIH)=6.359 E(NOE )=105.984 E(PLAN)=16.829 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.40 A apart NBONDS: found 63804 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 63733 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 63639 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63572 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63536 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 63507 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63548 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63593 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=1162.732 E(kin)=603.009 temperature=298.816 | | Etotal =559.723 grad(E)=72.157 E(BOND)=221.168 E(ANGL)=419.237 | | E(DIHE)=0.000 E(IMPR)=99.515 E(VDW )=-188.599 E(ELEC)=-139.282 | | E(CDIH)=3.047 E(NOE )=131.611 E(PLAN)=13.024 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63664 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63672 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63693 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63728 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63696 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63685 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart NBONDS: found 63627 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63602 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=1141.879 E(kin)=613.328 temperature=303.930 | | Etotal =528.551 grad(E)=66.347 E(BOND)=224.538 E(ANGL)=419.087 | | E(DIHE)=0.000 E(IMPR)=83.966 E(VDW )=-185.124 E(ELEC)=-147.939 | | E(CDIH)=7.886 E(NOE )=114.937 E(PLAN)=11.199 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1150.586 E(kin)=605.550 temperature=300.075 | | Etotal =545.036 grad(E)=69.803 E(BOND)=217.272 E(ANGL)=409.210 | | E(DIHE)=0.000 E(IMPR)=100.204 E(VDW )=-188.938 E(ELEC)=-140.225 | | E(CDIH)=5.205 E(NOE )=126.736 E(PLAN)=15.571 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.093 E(kin)=13.334 temperature=6.607 | | Etotal =15.921 grad(E)=2.136 E(BOND)=9.347 E(ANGL)=13.372 | | E(DIHE)=0.000 E(IMPR)=8.411 E(VDW )=8.154 E(ELEC)=4.521 | | E(CDIH)=2.249 E(NOE )=11.646 E(PLAN)=2.075 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=1150.897 E(kin)=605.244 temperature=299.924 | | Etotal =545.652 grad(E)=67.789 E(BOND)=218.386 E(ANGL)=403.160 | | E(DIHE)=0.000 E(IMPR)=96.380 E(VDW )=-185.910 E(ELEC)=-137.764 | | E(CDIH)=5.063 E(NOE )=130.200 E(PLAN)=16.136 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=17.733 E(kin)=14.100 temperature=6.987 | | Etotal =18.904 grad(E)=2.357 E(BOND)=11.468 E(ANGL)=14.448 | | E(DIHE)=0.000 E(IMPR)=8.096 E(VDW )=8.529 E(ELEC)=7.277 | | E(CDIH)=2.206 E(NOE )=11.250 E(PLAN)=2.294 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart NBONDS: found 63532 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 63378 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63382 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63365 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63408 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63514 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63562 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=1156.452 E(kin)=592.618 temperature=293.667 | | Etotal =563.834 grad(E)=68.518 E(BOND)=226.793 E(ANGL)=419.306 | | E(DIHE)=0.000 E(IMPR)=96.236 E(VDW )=-177.902 E(ELEC)=-144.546 | | E(CDIH)=3.416 E(NOE )=125.569 E(PLAN)=14.962 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 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 1.48 A apart NBONDS: found 63607 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63597 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart NBONDS: found 63630 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.44 A apart NBONDS: found 63616 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart NBONDS: found 63560 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63606 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63607 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=1163.481 E(kin)=618.030 temperature=306.260 | | Etotal =545.451 grad(E)=69.610 E(BOND)=206.483 E(ANGL)=425.572 | | E(DIHE)=0.000 E(IMPR)=103.213 E(VDW )=-180.601 E(ELEC)=-144.748 | | E(CDIH)=6.862 E(NOE )=114.829 E(PLAN)=13.841 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63573 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63583 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63583 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63632 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 63746 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63755 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 63779 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63781 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63761 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=1152.873 E(kin)=598.445 temperature=296.555 | | Etotal =554.427 grad(E)=69.672 E(BOND)=241.186 E(ANGL)=402.330 | | E(DIHE)=0.000 E(IMPR)=97.697 E(VDW )=-181.879 E(ELEC)=-146.222 | | E(CDIH)=0.722 E(NOE )=121.156 E(PLAN)=19.437 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63810 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63839 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63814 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63853 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63935 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63992 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64006 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=1140.305 E(kin)=595.056 temperature=294.875 | | Etotal =545.249 grad(E)=70.785 E(BOND)=229.205 E(ANGL)=426.362 | | E(DIHE)=0.000 E(IMPR)=89.143 E(VDW )=-185.769 E(ELEC)=-153.126 | | E(CDIH)=6.764 E(NOE )=118.352 E(PLAN)=14.318 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64017 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63997 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart NBONDS: found 63936 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63862 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63807 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63692 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart NBONDS: found 63677 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63634 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63627 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=1152.767 E(kin)=591.051 temperature=292.891 | | Etotal =561.716 grad(E)=72.021 E(BOND)=219.998 E(ANGL)=420.850 | | E(DIHE)=0.000 E(IMPR)=117.749 E(VDW )=-187.503 E(ELEC)=-147.139 | | E(CDIH)=4.012 E(NOE )=121.351 E(PLAN)=12.399 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63572 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart NBONDS: found 63603 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63607 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63695 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63740 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63759 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63794 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 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 1.49 A apart NBONDS: found 63756 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=1140.155 E(kin)=607.285 temperature=300.935 | | Etotal =532.871 grad(E)=68.557 E(BOND)=219.404 E(ANGL)=405.654 | | E(DIHE)=0.000 E(IMPR)=93.961 E(VDW )=-178.244 E(ELEC)=-153.616 | | E(CDIH)=5.337 E(NOE )=126.169 E(PLAN)=14.206 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63716 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63631 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63600 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63463 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63422 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63321 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63312 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63303 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=1132.421 E(kin)=604.322 temperature=299.467 | | Etotal =528.099 grad(E)=68.534 E(BOND)=215.374 E(ANGL)=390.486 | | E(DIHE)=0.000 E(IMPR)=99.425 E(VDW )=-181.192 E(ELEC)=-144.124 | | E(CDIH)=6.830 E(NOE )=123.328 E(PLAN)=17.972 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63330 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63268 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63272 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63198 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63147 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63111 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 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 1.48 A apart NBONDS: found 63058 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=1137.743 E(kin)=608.409 temperature=301.492 | | Etotal =529.334 grad(E)=66.331 E(BOND)=212.387 E(ANGL)=395.650 | | E(DIHE)=0.000 E(IMPR)=111.127 E(VDW )=-187.541 E(ELEC)=-148.991 | | E(CDIH)=9.575 E(NOE )=121.250 E(PLAN)=15.877 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63030 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62977 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62932 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62942 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62921 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62801 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=1156.600 E(kin)=608.463 temperature=301.519 | | Etotal =548.137 grad(E)=71.696 E(BOND)=209.118 E(ANGL)=412.219 | | E(DIHE)=0.000 E(IMPR)=114.769 E(VDW )=-188.828 E(ELEC)=-147.509 | | E(CDIH)=1.821 E(NOE )=124.141 E(PLAN)=22.407 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62694 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62598 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62598 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62620 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62699 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62809 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62923 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=1155.650 E(kin)=606.837 temperature=300.713 | | Etotal =548.813 grad(E)=66.842 E(BOND)=219.533 E(ANGL)=401.558 | | E(DIHE)=0.000 E(IMPR)=93.535 E(VDW )=-188.765 E(ELEC)=-143.395 | | E(CDIH)=5.843 E(NOE )=142.089 E(PLAN)=18.415 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1148.051 E(kin)=605.479 temperature=300.040 | | Etotal =542.572 grad(E)=69.700 E(BOND)=220.098 E(ANGL)=409.674 | | E(DIHE)=0.000 E(IMPR)=100.287 E(VDW )=-187.164 E(ELEC)=-147.214 | | E(CDIH)=5.023 E(NOE )=125.775 E(PLAN)=16.094 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.821 E(kin)=13.458 temperature=6.669 | | Etotal =16.559 grad(E)=2.369 E(BOND)=10.070 E(ANGL)=12.717 | | E(DIHE)=0.000 E(IMPR)=9.030 E(VDW )=7.890 E(ELEC)=4.393 | | E(CDIH)=2.085 E(NOE )=9.827 E(PLAN)=2.300 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=1150.581 E(kin)=605.271 temperature=299.937 | | Etotal =545.310 grad(E)=68.001 E(BOND)=218.576 E(ANGL)=403.884 | | E(DIHE)=0.000 E(IMPR)=96.814 E(VDW )=-186.049 E(ELEC)=-138.814 | | E(CDIH)=5.059 E(NOE )=129.708 E(PLAN)=16.132 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=17.060 E(kin)=14.030 temperature=6.953 | | Etotal =18.683 grad(E)=2.433 E(BOND)=11.334 E(ANGL)=14.412 | | E(DIHE)=0.000 E(IMPR)=8.297 E(VDW )=8.469 E(ELEC)=7.618 | | E(CDIH)=2.193 E(NOE )=11.188 E(PLAN)=2.294 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63019 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63182 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63351 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63380 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63357 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=1154.765 E(kin)=618.786 temperature=306.634 | | Etotal =535.979 grad(E)=67.777 E(BOND)=211.934 E(ANGL)=421.493 | | E(DIHE)=0.000 E(IMPR)=91.692 E(VDW )=-183.446 E(ELEC)=-143.295 | | E(CDIH)=3.341 E(NOE )=118.293 E(PLAN)=15.967 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63328 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63245 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63268 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63321 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63281 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63322 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63298 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=1161.553 E(kin)=611.394 temperature=302.971 | | Etotal =550.159 grad(E)=70.231 E(BOND)=223.998 E(ANGL)=408.426 | | E(DIHE)=0.000 E(IMPR)=95.950 E(VDW )=-191.351 E(ELEC)=-139.535 | | E(CDIH)=8.120 E(NOE )=130.207 E(PLAN)=14.343 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63299 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63308 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 63268 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 63266 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63307 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 63335 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=1157.091 E(kin)=629.403 temperature=311.896 | | Etotal =527.688 grad(E)=67.971 E(BOND)=210.732 E(ANGL)=404.504 | | E(DIHE)=0.000 E(IMPR)=94.629 E(VDW )=-193.448 E(ELEC)=-141.804 | | E(CDIH)=3.602 E(NOE )=130.764 E(PLAN)=18.709 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart NBONDS: found 63266 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63265 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63239 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63193 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63151 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63114 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63044 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62993 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 62991 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63025 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=1158.567 E(kin)=618.952 temperature=306.717 | | Etotal =539.616 grad(E)=68.812 E(BOND)=216.010 E(ANGL)=412.687 | | E(DIHE)=0.000 E(IMPR)=111.521 E(VDW )=-191.808 E(ELEC)=-149.985 | | E(CDIH)=1.311 E(NOE )=122.382 E(PLAN)=17.497 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 63018 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63033 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63115 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63212 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63212 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63253 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63268 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63287 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63324 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=1152.259 E(kin)=613.169 temperature=303.851 | | Etotal =539.090 grad(E)=66.833 E(BOND)=235.007 E(ANGL)=409.680 | | E(DIHE)=0.000 E(IMPR)=85.187 E(VDW )=-194.635 E(ELEC)=-143.978 | | E(CDIH)=10.126 E(NOE )=118.898 E(PLAN)=18.806 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63367 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63347 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63358 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63426 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63437 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63463 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63488 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63506 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63509 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=1144.091 E(kin)=606.225 temperature=300.410 | | Etotal =537.867 grad(E)=70.196 E(BOND)=202.625 E(ANGL)=427.332 | | E(DIHE)=0.000 E(IMPR)=99.112 E(VDW )=-188.742 E(ELEC)=-144.019 | | E(CDIH)=2.957 E(NOE )=120.094 E(PLAN)=18.507 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63506 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63618 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63608 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63623 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63631 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63639 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63593 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.45 A apart NBONDS: found 63595 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 63698 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=1145.838 E(kin)=595.421 temperature=295.056 | | Etotal =550.418 grad(E)=69.467 E(BOND)=222.181 E(ANGL)=409.923 | | E(DIHE)=0.000 E(IMPR)=101.923 E(VDW )=-185.332 E(ELEC)=-148.104 | | E(CDIH)=4.738 E(NOE )=127.244 E(PLAN)=17.846 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63730 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63742 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63727 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63770 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63782 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63806 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63820 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63858 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63894 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63886 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=1132.602 E(kin)=581.746 temperature=288.279 | | Etotal =550.856 grad(E)=69.501 E(BOND)=240.369 E(ANGL)=404.164 | | E(DIHE)=0.000 E(IMPR)=97.843 E(VDW )=-192.097 E(ELEC)=-150.657 | | E(CDIH)=4.403 E(NOE )=129.297 E(PLAN)=17.535 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart NBONDS: found 63907 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63960 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 63968 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart NBONDS: found 64037 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64096 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64145 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64178 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64194 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=1138.768 E(kin)=609.724 temperature=302.144 | | Etotal =529.045 grad(E)=66.563 E(BOND)=224.643 E(ANGL)=413.290 | | E(DIHE)=0.000 E(IMPR)=86.438 E(VDW )=-200.933 E(ELEC)=-147.596 | | E(CDIH)=4.629 E(NOE )=129.607 E(PLAN)=18.966 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 64307 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 64359 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 64380 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 64393 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 64397 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart NBONDS: found 64359 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64396 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=1145.006 E(kin)=588.377 temperature=291.566 | | Etotal =556.628 grad(E)=70.156 E(BOND)=230.780 E(ANGL)=418.295 | | E(DIHE)=0.000 E(IMPR)=102.420 E(VDW )=-194.853 E(ELEC)=-146.035 | | E(CDIH)=6.940 E(NOE )=126.024 E(PLAN)=13.058 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1147.480 E(kin)=605.566 temperature=300.084 | | Etotal =541.913 grad(E)=69.122 E(BOND)=219.973 E(ANGL)=410.655 | | E(DIHE)=0.000 E(IMPR)=99.156 E(VDW )=-189.611 E(ELEC)=-145.810 | | E(CDIH)=4.808 E(NOE )=126.947 E(PLAN)=15.795 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.038 E(kin)=13.598 temperature=6.738 | | Etotal =16.593 grad(E)=2.086 E(BOND)=9.820 E(ANGL)=14.060 | | E(DIHE)=0.000 E(IMPR)=8.516 E(VDW )=6.518 E(ELEC)=4.031 | | E(CDIH)=2.181 E(NOE )=9.523 E(PLAN)=1.782 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=1150.271 E(kin)=605.300 temperature=299.952 | | Etotal =544.970 grad(E)=68.113 E(BOND)=218.716 E(ANGL)=404.561 | | E(DIHE)=0.000 E(IMPR)=97.048 E(VDW )=-186.405 E(ELEC)=-139.513 | | E(CDIH)=5.034 E(NOE )=129.432 E(PLAN)=16.098 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=16.519 E(kin)=13.988 temperature=6.932 | | Etotal =18.513 grad(E)=2.424 E(BOND)=11.200 E(ANGL)=14.520 | | E(DIHE)=0.000 E(IMPR)=8.348 E(VDW )=8.363 E(ELEC)=7.633 | | E(CDIH)=2.193 E(NOE )=11.063 E(PLAN)=2.251 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 64434 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 64512 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 64632 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 64580 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64589 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64479 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=1167.684 E(kin)=617.746 temperature=306.119 | | Etotal =549.938 grad(E)=68.511 E(BOND)=232.469 E(ANGL)=421.604 | | E(DIHE)=0.000 E(IMPR)=91.242 E(VDW )=-191.852 E(ELEC)=-141.653 | | E(CDIH)=4.452 E(NOE )=119.859 E(PLAN)=13.818 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 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 1.47 A apart NBONDS: found 64428 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64412 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64399 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64356 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64393 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 64446 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64398 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 64444 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64415 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=1142.997 E(kin)=593.000 temperature=293.857 | | Etotal =549.996 grad(E)=70.844 E(BOND)=218.046 E(ANGL)=424.679 | | E(DIHE)=0.000 E(IMPR)=99.737 E(VDW )=-182.037 E(ELEC)=-146.727 | | E(CDIH)=2.384 E(NOE )=117.500 E(PLAN)=16.414 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 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 1.50 A apart NBONDS: found 64347 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64365 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64317 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 64308 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 64312 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64226 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 64157 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=1135.709 E(kin)=598.194 temperature=296.430 | | Etotal =537.515 grad(E)=69.764 E(BOND)=237.281 E(ANGL)=404.435 | | E(DIHE)=0.000 E(IMPR)=104.543 E(VDW )=-191.244 E(ELEC)=-151.560 | | E(CDIH)=6.853 E(NOE )=114.965 E(PLAN)=12.242 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64024 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63953 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63836 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63776 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63771 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63737 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63675 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63659 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63636 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63625 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=1145.827 E(kin)=620.226 temperature=307.348 | | Etotal =525.601 grad(E)=68.346 E(BOND)=221.760 E(ANGL)=406.477 | | E(DIHE)=0.000 E(IMPR)=99.752 E(VDW )=-189.222 E(ELEC)=-148.908 | | E(CDIH)=5.993 E(NOE )=112.507 E(PLAN)=17.242 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " 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 1.44 A apart NBONDS: found 63562 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63600 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63560 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63574 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63510 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63494 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63445 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63384 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=1149.965 E(kin)=609.607 temperature=302.086 | | Etotal =540.359 grad(E)=67.534 E(BOND)=226.310 E(ANGL)=404.508 | | E(DIHE)=0.000 E(IMPR)=96.207 E(VDW )=-191.821 E(ELEC)=-144.512 | | E(CDIH)=3.074 E(NOE )=132.155 E(PLAN)=14.437 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63215 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63100 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63034 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 62987 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 62936 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 62928 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=1144.800 E(kin)=602.230 temperature=298.430 | | Etotal =542.570 grad(E)=71.957 E(BOND)=208.046 E(ANGL)=424.045 | | E(DIHE)=0.000 E(IMPR)=109.706 E(VDW )=-196.444 E(ELEC)=-146.969 | | E(CDIH)=9.659 E(NOE )=118.759 E(PLAN)=15.768 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62947 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 62959 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62929 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63009 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63155 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63212 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63254 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=1161.000 E(kin)=593.386 temperature=294.048 | | Etotal =567.614 grad(E)=70.871 E(BOND)=235.487 E(ANGL)=421.693 | | E(DIHE)=0.000 E(IMPR)=106.666 E(VDW )=-187.957 E(ELEC)=-154.188 | | E(CDIH)=2.838 E(NOE )=125.524 E(PLAN)=17.551 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63203 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63171 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63080 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62988 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62969 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62945 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62943 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62896 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.49 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62868 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=1153.848 E(kin)=594.974 temperature=294.834 | | Etotal =558.874 grad(E)=70.112 E(BOND)=217.660 E(ANGL)=429.656 | | E(DIHE)=0.000 E(IMPR)=118.424 E(VDW )=-212.303 E(ELEC)=-138.607 | | E(CDIH)=4.438 E(NOE )=122.871 E(PLAN)=16.734 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 62836 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62851 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62869 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart NBONDS: found 62884 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 62884 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62956 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 62993 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63098 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63112 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63183 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63193 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=1144.563 E(kin)=605.007 temperature=299.806 | | Etotal =539.556 grad(E)=68.987 E(BOND)=228.214 E(ANGL)=406.093 | | E(DIHE)=0.000 E(IMPR)=88.022 E(VDW )=-176.635 E(ELEC)=-144.357 | | E(CDIH)=3.720 E(NOE )=120.969 E(PLAN)=13.531 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 63251 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63277 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63271 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63256 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63224 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63198 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63114 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 63033 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 62927 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62825 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62715 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=1155.808 E(kin)=597.462 temperature=296.068 | | Etotal =558.346 grad(E)=70.151 E(BOND)=216.722 E(ANGL)=416.767 | | E(DIHE)=0.000 E(IMPR)=97.071 E(VDW )=-182.821 E(ELEC)=-144.530 | | E(CDIH)=7.528 E(NOE )=130.912 E(PLAN)=16.696 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1147.685 E(kin)=605.476 temperature=300.039 | | Etotal =542.209 grad(E)=69.379 E(BOND)=220.082 E(ANGL)=410.638 | | E(DIHE)=0.000 E(IMPR)=99.182 E(VDW )=-189.348 E(ELEC)=-145.965 | | E(CDIH)=5.126 E(NOE )=126.875 E(PLAN)=15.621 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.271 E(kin)=13.112 temperature=6.497 | | Etotal =17.762 grad(E)=2.080 E(BOND)=9.943 E(ANGL)=12.973 | | E(DIHE)=0.000 E(IMPR)=7.709 E(VDW )=6.972 E(ELEC)=4.928 | | E(CDIH)=2.350 E(NOE )=9.208 E(PLAN)=1.919 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=1150.036 E(kin)=605.316 temperature=299.960 | | Etotal =544.719 grad(E)=68.229 E(BOND)=218.840 E(ANGL)=405.113 | | E(DIHE)=0.000 E(IMPR)=97.242 E(VDW )=-186.673 E(ELEC)=-140.100 | | E(CDIH)=5.042 E(NOE )=129.200 E(PLAN)=16.055 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=16.196 E(kin)=13.911 temperature=6.893 | | Etotal =18.463 grad(E)=2.423 E(BOND)=11.098 E(ANGL)=14.492 | | E(DIHE)=0.000 E(IMPR)=8.315 E(VDW )=8.290 E(ELEC)=7.656 | | E(CDIH)=2.208 E(NOE )=10.933 E(PLAN)=2.227 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62718 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62665 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62666 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62682 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 62700 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62639 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62763 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62837 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=1143.763 E(kin)=594.483 temperature=294.591 | | Etotal =549.280 grad(E)=70.663 E(BOND)=205.920 E(ANGL)=428.376 | | E(DIHE)=0.000 E(IMPR)=99.941 E(VDW )=-172.527 E(ELEC)=-143.111 | | E(CDIH)=1.697 E(NOE )=111.313 E(PLAN)=17.669 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62906 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62839 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62807 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62863 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 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 -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62847 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 62827 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=1156.585 E(kin)=588.794 temperature=291.772 | | Etotal =567.791 grad(E)=71.907 E(BOND)=222.370 E(ANGL)=411.201 | | E(DIHE)=0.000 E(IMPR)=108.722 E(VDW )=-185.407 E(ELEC)=-146.456 | | E(CDIH)=4.619 E(NOE )=139.439 E(PLAN)=13.304 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 62858 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 62857 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 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 1.40 A apart NBONDS: found 62849 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62758 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62720 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 62683 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 62709 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62708 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=1153.083 E(kin)=607.359 temperature=300.972 | | Etotal =545.724 grad(E)=66.761 E(BOND)=226.992 E(ANGL)=396.745 | | E(DIHE)=0.000 E(IMPR)=97.539 E(VDW )=-185.958 E(ELEC)=-138.554 | | E(CDIH)=7.806 E(NOE )=128.355 E(PLAN)=12.799 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62787 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62870 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62930 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62972 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63091 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 63120 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63180 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=1158.503 E(kin)=593.195 temperature=293.953 | | Etotal =565.308 grad(E)=70.265 E(BOND)=216.764 E(ANGL)=431.499 | | E(DIHE)=0.000 E(IMPR)=102.973 E(VDW )=-182.520 E(ELEC)=-142.971 | | E(CDIH)=6.718 E(NOE )=115.654 E(PLAN)=17.191 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63304 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63330 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63350 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63413 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63474 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63521 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 63497 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=1141.938 E(kin)=625.076 temperature=309.751 | | Etotal =516.862 grad(E)=69.243 E(BOND)=196.883 E(ANGL)=399.816 | | E(DIHE)=0.000 E(IMPR)=99.079 E(VDW )=-163.964 E(ELEC)=-152.754 | | E(CDIH)=2.605 E(NOE )=123.120 E(PLAN)=12.078 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 63429 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63394 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63377 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63346 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 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 1.45 A apart NBONDS: found 63340 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63309 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63302 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63321 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.34 A apart NBONDS: found 63344 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63392 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=1122.731 E(kin)=606.866 temperature=300.728 | | Etotal =515.865 grad(E)=65.565 E(BOND)=230.465 E(ANGL)=379.086 | | E(DIHE)=0.000 E(IMPR)=87.528 E(VDW )=-186.071 E(ELEC)=-143.100 | | E(CDIH)=4.867 E(NOE )=127.797 E(PLAN)=15.292 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63414 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63425 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63452 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63449 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63580 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.44 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 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 1.45 A apart NBONDS: found 63674 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63706 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63775 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63803 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 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 1.42 A apart NBONDS: found 63869 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63877 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=1134.020 E(kin)=611.902 temperature=303.223 | | Etotal =522.119 grad(E)=67.276 E(BOND)=204.334 E(ANGL)=408.339 | | E(DIHE)=0.000 E(IMPR)=98.124 E(VDW )=-193.003 E(ELEC)=-152.567 | | E(CDIH)=14.288 E(NOE )=125.617 E(PLAN)=16.986 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63891 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63876 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63806 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63708 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 63676 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63629 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 63600 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 63580 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 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 -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63703 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63660 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=1156.643 E(kin)=619.457 temperature=306.967 | | Etotal =537.186 grad(E)=66.748 E(BOND)=206.226 E(ANGL)=428.632 | | E(DIHE)=0.000 E(IMPR)=101.359 E(VDW )=-197.797 E(ELEC)=-144.575 | | E(CDIH)=2.225 E(NOE )=124.782 E(PLAN)=16.335 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63628 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 63603 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63643 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63603 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63606 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63698 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.23 A apart NBONDS: found 63794 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63958 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 64033 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=1148.481 E(kin)=597.421 temperature=296.047 | | Etotal =551.060 grad(E)=68.576 E(BOND)=228.013 E(ANGL)=405.520 | | E(DIHE)=0.000 E(IMPR)=107.529 E(VDW )=-184.653 E(ELEC)=-152.195 | | E(CDIH)=4.922 E(NOE )=127.400 E(PLAN)=14.524 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart NBONDS: found 64115 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart NBONDS: found 64140 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64136 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64099 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64067 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64016 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63945 intra-atom interactions %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63886 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63845 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.49 A apart NBONDS: found 63810 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=1139.488 E(kin)=614.073 temperature=304.299 | | Etotal =525.414 grad(E)=67.407 E(BOND)=218.289 E(ANGL)=405.733 | | E(DIHE)=0.000 E(IMPR)=97.329 E(VDW )=-200.711 E(ELEC)=-141.527 | | E(CDIH)=2.309 E(NOE )=128.659 E(PLAN)=15.333 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1145.576 E(kin)=605.571 temperature=300.086 | | Etotal =540.005 grad(E)=68.577 E(BOND)=217.586 E(ANGL)=407.869 | | E(DIHE)=0.000 E(IMPR)=99.037 E(VDW )=-186.906 E(ELEC)=-145.993 | | E(CDIH)=5.426 E(NOE )=126.875 E(PLAN)=16.110 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.737 E(kin)=13.094 temperature=6.489 | | Etotal =16.714 grad(E)=2.105 E(BOND)=9.956 E(ANGL)=13.132 | | E(DIHE)=0.000 E(IMPR)=8.286 E(VDW )=8.624 E(ELEC)=4.901 | | E(CDIH)=2.363 E(NOE )=9.802 E(PLAN)=2.141 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=1149.664 E(kin)=605.337 temperature=299.970 | | Etotal =544.327 grad(E)=68.258 E(BOND)=218.736 E(ANGL)=405.343 | | E(DIHE)=0.000 E(IMPR)=97.392 E(VDW )=-186.692 E(ELEC)=-140.591 | | E(CDIH)=5.074 E(NOE )=129.006 E(PLAN)=16.059 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=15.861 E(kin)=13.845 temperature=6.861 | | Etotal =18.370 grad(E)=2.400 E(BOND)=11.013 E(ANGL)=14.403 | | E(DIHE)=0.000 E(IMPR)=8.327 E(VDW )=8.319 E(ELEC)=7.641 | | E(CDIH)=2.224 E(NOE )=10.862 E(PLAN)=2.220 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart NBONDS: found 63777 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.46 A apart NBONDS: found 63750 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63742 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63683 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart NBONDS: found 63708 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63718 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63781 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63846 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63920 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63938 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=1148.694 E(kin)=604.702 temperature=299.655 | | Etotal =543.992 grad(E)=68.041 E(BOND)=203.812 E(ANGL)=401.866 | | E(DIHE)=0.000 E(IMPR)=114.141 E(VDW )=-179.326 E(ELEC)=-158.051 | | E(CDIH)=7.522 E(NOE )=138.231 E(PLAN)=15.795 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63974 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63959 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63975 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63939 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63903 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63825 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63720 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63585 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 63546 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 63503 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=1133.999 E(kin)=600.306 temperature=297.477 | | Etotal =533.693 grad(E)=70.429 E(BOND)=225.189 E(ANGL)=401.023 | | E(DIHE)=0.000 E(IMPR)=99.718 E(VDW )=-202.830 E(ELEC)=-148.140 | | E(CDIH)=4.723 E(NOE )=139.587 E(PLAN)=14.422 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.47 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63452 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart NBONDS: found 63436 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63567 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart NBONDS: found 63535 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63644 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart NBONDS: found 63580 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=1147.317 E(kin)=614.781 temperature=304.650 | | Etotal =532.536 grad(E)=67.314 E(BOND)=212.015 E(ANGL)=418.291 | | E(DIHE)=0.000 E(IMPR)=97.057 E(VDW )=-199.625 E(ELEC)=-150.361 | | E(CDIH)=6.362 E(NOE )=133.001 E(PLAN)=15.796 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 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 1.50 A apart NBONDS: found 63519 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63470 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63456 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63416 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 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 -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63466 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=1139.309 E(kin)=598.792 temperature=296.727 | | Etotal =540.517 grad(E)=69.651 E(BOND)=223.514 E(ANGL)=410.502 | | E(DIHE)=0.000 E(IMPR)=109.143 E(VDW )=-187.979 E(ELEC)=-137.566 | | E(CDIH)=3.038 E(NOE )=107.034 E(PLAN)=12.831 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63427 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart NBONDS: found 63494 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63517 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.50 A apart NBONDS: found 63551 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63535 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=1156.864 E(kin)=595.578 temperature=295.134 | | Etotal =561.286 grad(E)=69.671 E(BOND)=233.548 E(ANGL)=422.731 | | E(DIHE)=0.000 E(IMPR)=98.458 E(VDW )=-192.603 E(ELEC)=-140.224 | | E(CDIH)=4.722 E(NOE )=119.914 E(PLAN)=14.740 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 63516 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 63428 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63396 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63387 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63362 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63330 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 63315 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=1153.499 E(kin)=591.976 temperature=293.349 | | Etotal =561.523 grad(E)=69.524 E(BOND)=236.982 E(ANGL)=416.339 | | E(DIHE)=0.000 E(IMPR)=95.781 E(VDW )=-183.203 E(ELEC)=-143.930 | | E(CDIH)=2.244 E(NOE )=124.161 E(PLAN)=13.150 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.24 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63294 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart NBONDS: found 63238 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63200 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 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 -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63183 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63081 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63032 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=1142.911 E(kin)=602.033 temperature=298.333 | | Etotal =540.878 grad(E)=69.381 E(BOND)=229.398 E(ANGL)=411.579 | | E(DIHE)=0.000 E(IMPR)=96.612 E(VDW )=-184.085 E(ELEC)=-144.086 | | E(CDIH)=4.131 E(NOE )=113.778 E(PLAN)=13.551 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 62978 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62912 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62873 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62934 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62999 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 62990 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=1155.421 E(kin)=629.851 temperature=312.117 | | Etotal =525.570 grad(E)=68.982 E(BOND)=208.444 E(ANGL)=405.930 | | E(DIHE)=0.000 E(IMPR)=98.843 E(VDW )=-203.481 E(ELEC)=-145.083 | | E(CDIH)=7.500 E(NOE )=139.748 E(PLAN)=13.669 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 63040 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart NBONDS: found 63066 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 63117 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63157 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63206 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart NBONDS: found 63259 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63336 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=1157.047 E(kin)=598.785 temperature=296.723 | | Etotal =558.262 grad(E)=70.425 E(BOND)=227.803 E(ANGL)=419.492 | | E(DIHE)=0.000 E(IMPR)=96.690 E(VDW )=-190.543 E(ELEC)=-146.819 | | E(CDIH)=10.573 E(NOE )=123.016 E(PLAN)=18.050 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63333 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63289 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart NBONDS: found 63278 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63367 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 63427 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=1141.046 E(kin)=578.902 temperature=286.870 | | Etotal =562.145 grad(E)=72.184 E(BOND)=240.149 E(ANGL)=411.640 | | E(DIHE)=0.000 E(IMPR)=96.876 E(VDW )=-192.675 E(ELEC)=-143.249 | | E(CDIH)=5.762 E(NOE )=129.259 E(PLAN)=14.383 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1147.132 E(kin)=605.502 temperature=300.052 | | Etotal =541.630 grad(E)=68.862 E(BOND)=219.843 E(ANGL)=412.035 | | E(DIHE)=0.000 E(IMPR)=97.085 E(VDW )=-190.197 E(ELEC)=-145.821 | | E(CDIH)=5.046 E(NOE )=127.633 E(PLAN)=16.005 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.113 E(kin)=13.514 temperature=6.697 | | Etotal =16.603 grad(E)=2.038 E(BOND)=11.571 E(ANGL)=12.953 | | E(DIHE)=0.000 E(IMPR)=7.910 E(VDW )=7.452 E(ELEC)=5.989 | | E(CDIH)=2.205 E(NOE )=10.988 E(PLAN)=1.726 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=1149.469 E(kin)=605.350 temperature=299.976 | | Etotal =544.119 grad(E)=68.304 E(BOND)=218.821 E(ANGL)=405.858 | | E(DIHE)=0.000 E(IMPR)=97.368 E(VDW )=-186.962 E(ELEC)=-140.993 | | E(CDIH)=5.072 E(NOE )=128.901 E(PLAN)=16.055 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=15.510 E(kin)=13.819 temperature=6.848 | | Etotal =18.254 grad(E)=2.379 E(BOND)=11.061 E(ANGL)=14.408 | | E(DIHE)=0.000 E(IMPR)=8.296 E(VDW )=8.308 E(ELEC)=7.655 | | E(CDIH)=2.222 E(NOE )=10.878 E(PLAN)=2.186 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 63426 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63504 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 63559 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 63624 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63658 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63666 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=1125.708 E(kin)=603.353 temperature=298.987 | | Etotal =522.355 grad(E)=67.496 E(BOND)=235.752 E(ANGL)=395.631 | | E(DIHE)=0.000 E(IMPR)=87.132 E(VDW )=-177.770 E(ELEC)=-143.852 | | E(CDIH)=3.723 E(NOE )=106.393 E(PLAN)=15.346 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63714 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63701 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 63682 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63724 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63790 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=1153.257 E(kin)=579.454 temperature=287.144 | | Etotal =573.803 grad(E)=71.926 E(BOND)=222.435 E(ANGL)=425.113 | | E(DIHE)=0.000 E(IMPR)=102.398 E(VDW )=-176.886 E(ELEC)=-139.550 | | E(CDIH)=11.587 E(NOE )=112.903 E(PLAN)=15.804 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 63889 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 63931 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63996 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63980 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=1146.742 E(kin)=609.027 temperature=301.798 | | Etotal =537.715 grad(E)=68.222 E(BOND)=244.454 E(ANGL)=400.083 | | E(DIHE)=0.000 E(IMPR)=94.766 E(VDW )=-187.667 E(ELEC)=-148.983 | | E(CDIH)=3.082 E(NOE )=115.910 E(PLAN)=16.070 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64003 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63885 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63840 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 63642 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.41 A apart NBONDS: found 63575 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63510 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=1148.058 E(kin)=612.319 temperature=303.430 | | Etotal =535.739 grad(E)=68.586 E(BOND)=221.630 E(ANGL)=396.203 | | E(DIHE)=0.000 E(IMPR)=100.676 E(VDW )=-187.468 E(ELEC)=-143.970 | | E(CDIH)=2.323 E(NOE )=132.296 E(PLAN)=14.048 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63510 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart NBONDS: found 63500 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63528 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63544 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=1148.618 E(kin)=632.007 temperature=313.186 | | Etotal =516.610 grad(E)=68.963 E(BOND)=202.060 E(ANGL)=404.304 | | E(DIHE)=0.000 E(IMPR)=101.847 E(VDW )=-196.663 E(ELEC)=-146.991 | | E(CDIH)=4.714 E(NOE )=131.868 E(PLAN)=15.472 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 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 -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63637 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart NBONDS: found 63648 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart NBONDS: found 63713 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 63683 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=1136.399 E(kin)=606.365 temperature=300.479 | | Etotal =530.034 grad(E)=68.640 E(BOND)=202.510 E(ANGL)=409.784 | | E(DIHE)=0.000 E(IMPR)=113.144 E(VDW )=-198.447 E(ELEC)=-146.006 | | E(CDIH)=3.612 E(NOE )=132.147 E(PLAN)=13.290 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63787 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63917 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63980 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64041 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=1156.090 E(kin)=604.270 temperature=299.441 | | Etotal =551.820 grad(E)=72.238 E(BOND)=243.834 E(ANGL)=394.397 | | E(DIHE)=0.000 E(IMPR)=103.556 E(VDW )=-180.820 E(ELEC)=-147.273 | | E(CDIH)=1.296 E(NOE )=119.540 E(PLAN)=17.291 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64051 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63924 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63924 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63819 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63698 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=1148.844 E(kin)=627.193 temperature=310.801 | | Etotal =521.651 grad(E)=69.562 E(BOND)=208.291 E(ANGL)=415.299 | | E(DIHE)=0.000 E(IMPR)=99.048 E(VDW )=-189.786 E(ELEC)=-148.238 | | E(CDIH)=3.543 E(NOE )=120.073 E(PLAN)=13.420 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63603 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 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 -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63340 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63218 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=1160.373 E(kin)=621.527 temperature=307.993 | | Etotal =538.847 grad(E)=71.382 E(BOND)=224.838 E(ANGL)=396.630 | | E(DIHE)=0.000 E(IMPR)=110.017 E(VDW )=-184.226 E(ELEC)=-160.718 | | E(CDIH)=4.412 E(NOE )=129.783 E(PLAN)=18.110 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63107 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63067 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62968 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62954 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62993 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63042 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=1144.945 E(kin)=581.978 temperature=288.394 | | Etotal =562.967 grad(E)=73.447 E(BOND)=220.019 E(ANGL)=423.726 | | E(DIHE)=0.000 E(IMPR)=108.369 E(VDW )=-184.346 E(ELEC)=-156.792 | | E(CDIH)=2.626 E(NOE )=126.366 E(PLAN)=23.000 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1147.734 E(kin)=605.507 temperature=300.054 | | Etotal =542.227 grad(E)=69.585 E(BOND)=223.070 E(ANGL)=408.819 | | E(DIHE)=0.000 E(IMPR)=100.870 E(VDW )=-190.593 E(ELEC)=-148.037 | | E(CDIH)=4.778 E(NOE )=127.328 E(PLAN)=15.991 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.042 E(kin)=13.224 temperature=6.553 | | Etotal =16.398 grad(E)=2.159 E(BOND)=10.313 E(ANGL)=13.359 | | E(DIHE)=0.000 E(IMPR)=8.445 E(VDW )=7.649 E(ELEC)=4.446 | | E(CDIH)=2.131 E(NOE )=10.628 E(PLAN)=2.195 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=1149.345 E(kin)=605.361 temperature=299.982 | | Etotal =543.984 grad(E)=68.396 E(BOND)=219.124 E(ANGL)=406.069 | | E(DIHE)=0.000 E(IMPR)=97.618 E(VDW )=-187.221 E(ELEC)=-141.496 | | E(CDIH)=5.051 E(NOE )=128.788 E(PLAN)=16.051 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=15.191 E(kin)=13.778 temperature=6.827 | | Etotal =18.134 grad(E)=2.387 E(BOND)=11.063 E(ANGL)=14.356 | | E(DIHE)=0.000 E(IMPR)=8.356 E(VDW )=8.315 E(ELEC)=7.689 | | E(CDIH)=2.217 E(NOE )=10.868 E(PLAN)=2.187 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63023 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63098 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63128 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63199 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63311 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=1145.885 E(kin)=604.059 temperature=299.337 | | Etotal =541.826 grad(E)=68.971 E(BOND)=224.678 E(ANGL)=408.912 | | E(DIHE)=0.000 E(IMPR)=93.112 E(VDW )=-186.546 E(ELEC)=-148.101 | | E(CDIH)=2.922 E(NOE )=130.910 E(PLAN)=15.938 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63439 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63489 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63453 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63480 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63500 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 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 1.45 A apart NBONDS: found 63553 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=1135.709 E(kin)=616.859 temperature=305.680 | | Etotal =518.849 grad(E)=66.209 E(BOND)=214.165 E(ANGL)=405.505 | | E(DIHE)=0.000 E(IMPR)=92.122 E(VDW )=-193.440 E(ELEC)=-152.570 | | E(CDIH)=7.624 E(NOE )=127.133 E(PLAN)=18.309 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63609 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63589 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63616 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63678 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63726 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63828 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=1143.468 E(kin)=616.092 temperature=305.299 | | Etotal =527.376 grad(E)=68.160 E(BOND)=222.506 E(ANGL)=386.088 | | E(DIHE)=0.000 E(IMPR)=96.180 E(VDW )=-176.112 E(ELEC)=-147.897 | | E(CDIH)=5.052 E(NOE )=127.778 E(PLAN)=13.782 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63965 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 64030 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64050 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64069 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 64068 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 64066 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 64071 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=1145.720 E(kin)=599.329 temperature=296.993 | | Etotal =546.390 grad(E)=71.637 E(BOND)=214.611 E(ANGL)=404.775 | | E(DIHE)=0.000 E(IMPR)=110.769 E(VDW )=-186.890 E(ELEC)=-147.574 | | E(CDIH)=4.922 E(NOE )=134.494 E(PLAN)=11.282 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 64028 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.45 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart NBONDS: found 64052 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 64039 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 64039 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart NBONDS: found 64106 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 64175 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart NBONDS: found 64183 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=1151.098 E(kin)=594.312 temperature=294.507 | | Etotal =556.786 grad(E)=73.119 E(BOND)=226.529 E(ANGL)=411.889 | | E(DIHE)=0.000 E(IMPR)=101.778 E(VDW )=-208.287 E(ELEC)=-140.923 | | E(CDIH)=3.358 E(NOE )=147.593 E(PLAN)=14.849 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart NBONDS: found 64149 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 64168 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64219 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64216 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 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 1.42 A apart NBONDS: found 64192 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=1152.107 E(kin)=610.204 temperature=302.382 | | Etotal =541.903 grad(E)=67.376 E(BOND)=219.781 E(ANGL)=400.470 | | E(DIHE)=0.000 E(IMPR)=105.733 E(VDW )=-191.384 E(ELEC)=-146.936 | | E(CDIH)=5.465 E(NOE )=134.389 E(PLAN)=14.383 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64043 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63856 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart NBONDS: found 63642 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.35 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63443 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=1145.216 E(kin)=605.045 temperature=299.825 | | Etotal =540.171 grad(E)=68.971 E(BOND)=212.072 E(ANGL)=395.546 | | E(DIHE)=0.000 E(IMPR)=100.753 E(VDW )=-190.121 E(ELEC)=-148.948 | | E(CDIH)=6.670 E(NOE )=150.619 E(PLAN)=13.581 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63389 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63274 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63208 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.32 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 1.49 A apart NBONDS: found 63230 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63293 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 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 1.44 A apart NBONDS: found 63318 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=1148.527 E(kin)=589.952 temperature=292.346 | | Etotal =558.576 grad(E)=71.911 E(BOND)=200.644 E(ANGL)=406.575 | | E(DIHE)=0.000 E(IMPR)=117.468 E(VDW )=-173.075 E(ELEC)=-150.625 | | E(CDIH)=4.848 E(NOE )=134.318 E(PLAN)=18.422 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63343 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63311 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63224 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63103 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62958 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=1139.176 E(kin)=616.642 temperature=305.572 | | Etotal =522.534 grad(E)=68.442 E(BOND)=212.403 E(ANGL)=384.051 | | E(DIHE)=0.000 E(IMPR)=116.387 E(VDW )=-182.468 E(ELEC)=-154.340 | | E(CDIH)=7.038 E(NOE )=126.660 E(PLAN)=12.803 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62859 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62804 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62851 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart NBONDS: found 62952 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63067 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63152 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63227 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=1154.673 E(kin)=607.687 temperature=301.134 | | Etotal =546.986 grad(E)=67.801 E(BOND)=222.396 E(ANGL)=420.439 | | E(DIHE)=0.000 E(IMPR)=97.897 E(VDW )=-173.846 E(ELEC)=-149.811 | | E(CDIH)=4.383 E(NOE )=106.642 E(PLAN)=18.885 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1146.239 E(kin)=605.505 temperature=300.053 | | Etotal =540.734 grad(E)=69.851 E(BOND)=220.798 E(ANGL)=402.013 | | E(DIHE)=0.000 E(IMPR)=104.988 E(VDW )=-189.851 E(ELEC)=-149.055 | | E(CDIH)=5.076 E(NOE )=131.076 E(PLAN)=15.690 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.792 E(kin)=13.218 temperature=6.550 | | Etotal =15.854 grad(E)=2.417 E(BOND)=9.729 E(ANGL)=13.303 | | E(DIHE)=0.000 E(IMPR)=9.405 E(VDW )=8.004 E(ELEC)=3.864 | | E(CDIH)=2.165 E(NOE )=10.621 E(PLAN)=2.182 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=1149.138 E(kin)=605.371 temperature=299.987 | | Etotal =543.767 grad(E)=68.493 E(BOND)=219.236 E(ANGL)=405.799 | | E(DIHE)=0.000 E(IMPR)=98.110 E(VDW )=-187.397 E(ELEC)=-142.000 | | E(CDIH)=5.053 E(NOE )=128.941 E(PLAN)=16.026 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=14.871 E(kin)=13.741 temperature=6.809 | | Etotal =18.010 grad(E)=2.417 E(BOND)=10.987 E(ANGL)=14.324 | | E(DIHE)=0.000 E(IMPR)=8.628 E(VDW )=8.321 E(ELEC)=7.728 | | E(CDIH)=2.214 E(NOE )=10.866 E(PLAN)=2.188 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 63289 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63397 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63405 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 63556 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=1141.747 E(kin)=610.977 temperature=302.765 | | Etotal =530.770 grad(E)=67.384 E(BOND)=220.858 E(ANGL)=394.017 | | E(DIHE)=0.000 E(IMPR)=96.059 E(VDW )=-176.745 E(ELEC)=-150.706 | | E(CDIH)=7.752 E(NOE )=126.900 E(PLAN)=12.634 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63584 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63483 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63389 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63230 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=1138.068 E(kin)=604.432 temperature=299.521 | | Etotal =533.636 grad(E)=67.058 E(BOND)=227.470 E(ANGL)=415.696 | | E(DIHE)=0.000 E(IMPR)=90.435 E(VDW )=-181.524 E(ELEC)=-146.744 | | E(CDIH)=6.442 E(NOE )=106.168 E(PLAN)=15.692 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63190 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart NBONDS: found 63186 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63286 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63317 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63344 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=1154.522 E(kin)=584.729 temperature=289.758 | | Etotal =569.793 grad(E)=73.930 E(BOND)=231.512 E(ANGL)=404.735 | | E(DIHE)=0.000 E(IMPR)=115.265 E(VDW )=-185.902 E(ELEC)=-148.054 | | E(CDIH)=4.777 E(NOE )=129.139 E(PLAN)=18.320 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 63363 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63352 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63363 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63342 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=1143.056 E(kin)=611.846 temperature=303.195 | | Etotal =531.210 grad(E)=72.537 E(BOND)=218.992 E(ANGL)=380.907 | | E(DIHE)=0.000 E(IMPR)=115.897 E(VDW )=-196.505 E(ELEC)=-148.959 | | E(CDIH)=3.032 E(NOE )=139.948 E(PLAN)=17.897 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart NBONDS: found 63348 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.38 A apart NBONDS: found 63405 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63590 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63656 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 63729 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=1132.948 E(kin)=588.010 temperature=291.384 | | Etotal =544.938 grad(E)=69.684 E(BOND)=237.593 E(ANGL)=381.246 | | E(DIHE)=0.000 E(IMPR)=108.777 E(VDW )=-196.687 E(ELEC)=-148.442 | | E(CDIH)=7.035 E(NOE )=140.166 E(PLAN)=15.250 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63795 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart NBONDS: found 63873 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64027 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64055 intra-atom interactions %atoms "A -10 -CYT -H5' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64102 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64087 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=1133.508 E(kin)=618.088 temperature=306.288 | | Etotal =515.420 grad(E)=67.839 E(BOND)=226.359 E(ANGL)=402.405 | | E(DIHE)=0.000 E(IMPR)=97.716 E(VDW )=-190.795 E(ELEC)=-152.447 | | E(CDIH)=5.190 E(NOE )=112.976 E(PLAN)=14.017 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64057 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 63964 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63808 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63763 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 63729 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63714 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=1143.690 E(kin)=618.250 temperature=306.369 | | Etotal =525.439 grad(E)=70.807 E(BOND)=214.231 E(ANGL)=400.557 | | E(DIHE)=0.000 E(IMPR)=102.233 E(VDW )=-196.784 E(ELEC)=-153.033 | | E(CDIH)=3.405 E(NOE )=139.027 E(PLAN)=15.804 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart NBONDS: found 63703 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.35 A apart NBONDS: found 63749 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.34 A apart NBONDS: found 63740 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63735 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 63750 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.48 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 63716 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=1158.659 E(kin)=605.555 temperature=300.078 | | Etotal =553.103 grad(E)=71.541 E(BOND)=215.553 E(ANGL)=412.872 | | E(DIHE)=0.000 E(IMPR)=116.715 E(VDW )=-193.431 E(ELEC)=-144.916 | | E(CDIH)=6.832 E(NOE )=123.261 E(PLAN)=16.216 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.41 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 63686 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.43 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.36 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 63679 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63705 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.36 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63685 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 63705 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 63719 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.30 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 63765 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63765 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=1141.411 E(kin)=591.618 temperature=293.171 | | Etotal =549.794 grad(E)=73.913 E(BOND)=216.485 E(ANGL)=414.478 | | E(DIHE)=0.000 E(IMPR)=112.672 E(VDW )=-195.624 E(ELEC)=-150.784 | | E(CDIH)=3.066 E(NOE )=134.709 E(PLAN)=14.792 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.32 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63785 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.37 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63823 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.25 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 63812 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.29 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.35 A apart NBONDS: found 63798 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.31 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 63746 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 63700 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.28 A apart %atoms "A -10 -CYT -O4' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 63686 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=1132.638 E(kin)=597.213 temperature=295.944 | | Etotal =535.425 grad(E)=69.811 E(BOND)=211.432 E(ANGL)=401.964 | | E(DIHE)=0.000 E(IMPR)=105.528 E(VDW )=-180.248 E(ELEC)=-157.386 | | E(CDIH)=1.727 E(NOE )=135.624 E(PLAN)=16.784 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1145.871 E(kin)=605.607 temperature=300.104 | | Etotal =540.264 grad(E)=70.298 E(BOND)=222.736 E(ANGL)=400.937 | | E(DIHE)=0.000 E(IMPR)=105.783 E(VDW )=-186.720 E(ELEC)=-151.031 | | E(CDIH)=5.136 E(NOE )=127.492 E(PLAN)=15.930 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.867 E(kin)=13.150 temperature=6.516 | | Etotal =15.748 grad(E)=2.426 E(BOND)=10.054 E(ANGL)=12.308 | | E(DIHE)=0.000 E(IMPR)=9.229 E(VDW )=7.567 E(ELEC)=4.234 | | E(CDIH)=2.263 E(NOE )=11.040 E(PLAN)=1.879 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=1148.934 E(kin)=605.386 temperature=299.994 | | Etotal =543.548 grad(E)=68.605 E(BOND)=219.455 E(ANGL)=405.495 | | E(DIHE)=0.000 E(IMPR)=98.589 E(VDW )=-187.354 E(ELEC)=-142.565 | | E(CDIH)=5.058 E(NOE )=128.850 E(PLAN)=16.020 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=14.590 E(kin)=13.705 temperature=6.791 | | Etotal =17.897 grad(E)=2.456 E(BOND)=10.964 E(ANGL)=14.255 | | E(DIHE)=0.000 E(IMPR)=8.864 E(VDW )=8.277 E(ELEC)=7.867 | | E(CDIH)=2.217 E(NOE )=10.883 E(PLAN)=2.170 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.08478 0.04526 0.00909 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 05:29:46 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 -H4' " and "A -11 -ADE -O5' " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 63540 intra-atom interactions %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63539 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =-25.184 grad(E)=7.558 E(BOND)=23.851 E(ANGL)=174.605 | | E(DIHE)=0.000 E(IMPR)=19.440 E(VDW )=-193.117 E(ELEC)=-155.062 | | E(CDIH)=3.780 E(NOE )=87.631 E(PLAN)=13.687 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.48 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 63529 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =-63.699 grad(E)=2.422 E(BOND)=14.893 E(ANGL)=145.940 | | E(DIHE)=0.000 E(IMPR)=17.881 E(VDW )=-195.139 E(ELEC)=-153.692 | | E(CDIH)=3.821 E(NOE )=89.467 E(PLAN)=13.130 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =-67.970 grad(E)=3.024 E(BOND)=14.534 E(ANGL)=145.613 | | E(DIHE)=0.000 E(IMPR)=16.872 E(VDW )=-197.448 E(ELEC)=-155.334 | | E(CDIH)=3.652 E(NOE )=91.829 E(PLAN)=12.312 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =-70.213 grad(E)=1.413 E(BOND)=14.659 E(ANGL)=145.690 | | E(DIHE)=0.000 E(IMPR)=16.751 E(VDW )=-198.630 E(ELEC)=-157.233 | | E(CDIH)=3.667 E(NOE )=93.068 E(PLAN)=11.817 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =-72.510 grad(E)=1.191 E(BOND)=14.555 E(ANGL)=145.211 | | E(DIHE)=0.000 E(IMPR)=16.587 E(VDW )=-198.382 E(ELEC)=-159.430 | | E(CDIH)=3.746 E(NOE )=93.564 E(PLAN)=11.641 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =-74.126 grad(E)=1.275 E(BOND)=14.316 E(ANGL)=145.579 | | E(DIHE)=0.000 E(IMPR)=16.576 E(VDW )=-198.790 E(ELEC)=-161.012 | | E(CDIH)=3.807 E(NOE )=93.815 E(PLAN)=11.582 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =-75.682 grad(E)=0.901 E(BOND)=14.147 E(ANGL)=146.656 | | E(DIHE)=0.000 E(IMPR)=16.695 E(VDW )=-199.559 E(ELEC)=-162.813 | | E(CDIH)=3.899 E(NOE )=93.702 E(PLAN)=11.592 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =-76.509 grad(E)=0.884 E(BOND)=14.155 E(ANGL)=146.412 | | E(DIHE)=0.000 E(IMPR)=16.693 E(VDW )=-199.130 E(ELEC)=-163.401 | | E(CDIH)=3.743 E(NOE )=93.281 E(PLAN)=11.739 | ------------------------------------------------------------------------------- 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 $RMS_BOND set to 0.296846E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (A 9 C4' |A 9 C3' |A 9 O3' ) 116.031 110.500 5.531 4.147 445.032 (A 9 C2' |A 9 C3' |A 9 O3' ) 105.420 111.000 -5.580 3.639 383.726 (A 10 C5' |A 10 C4' |A 10 C3' ) 109.418 115.500 -6.082 5.509 488.878 (A 10 O4' |A 10 C1' |A 10 C2' ) 101.108 106.400 -5.292 4.787 561.212 (A 10 C2' |A 10 C3' |A 10 O3' ) 116.408 111.000 5.408 3.419 383.726 (A 11 O4' |A 11 C4' |A 11 C3' ) 98.511 105.500 -6.989 8.350 561.212 Number of violations greater 5.000: 6 RMS deviation= 0.834 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.833630 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 6.00000 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.413 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.413440 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 9 URI H2' set-j-atoms A 11 ADE H8 R= 4.348 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.348 E(NOE)= 12.100 ======================================== set-i-atoms A 10 CYT H2' set-j-atoms A 11 ADE H8 R= 3.218 NOE= 2.40 (- 0.60/+ 0.60) Delta= -0.218 E(NOE)= 4.735 ======================================== set-i-atoms A 10 CYT H3' set-j-atoms A 11 ADE H8 R= 3.534 NOE= 2.40 (- 0.60/+ 0.60) Delta= -0.534 E(NOE)= 28.473 ======================================== set-i-atoms A 11 ADE H8 set-j-atoms A 11 ADE H3' R= 3.253 NOE= 2.40 (- 0.60/+ 0.60) Delta= -0.253 E(NOE)= 6.419 ======================================== set-i-atoms A 12 URI H6 set-j-atoms A 12 URI H3' R= 4.248 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.248 E(NOE)= 6.167 NOEPRI: RMS diff. = 0.032, #(violat.> 0.2)= 5 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.032, #(viol.> 0.2)= 5 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.317046E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 5.00000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 0 RMS deviation= 0.275 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.275080 (real) X-PLOR>evaluate ($v_cdih=$violations) EVALUATE: symbol $V_CDIH set to 0.000000E+00 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 14.1555, angle 146.412, dihedral 0, improper 16.6931, NOE 93.2807, c-dihedral 3.74333, planar 11.7385, VdW -199.13, elec -163.401, total -76.5086 RMSD: bond 2.968463E-03, angle 0.83363, dihedral 0, improper 0.41344, NOE 3.170457E-02, c-dihedral 0.27508 Violations: bond 0, angle 6, dihedral 0, improper 0, NOE 5, c-dihedral 0 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= 135126 current use= 0 X-PLOR: total CPU time= 2983.7256 s X-PLOR: entry time at 05:29:15 17-Aug-96 X-PLOR: exit time at 06:19:14 17-Aug-96