X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 00:18:34 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=29042.1540527344 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 17:39:16 created by user: COOR>ATOM 1 P GUA A 1 -2.729 12.801 -2.636 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -1.791 13.952 -2.684 1.00 0.00 A X-PLOR> ! END in PDB file X-PLOR> X-PLOR>flags exclude * include bond angl dihe impr vdw elec noe cdih plan end X-PLOR> X-PLOR>! Intial minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2090 exclusions and 1650 interactions(1-4) %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 64498 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =97.598 grad(E)=5.375 E(BOND)=18.665 E(ANGL)=146.501 | | E(DIHE)=0.000 E(IMPR)=18.683 E(VDW )=-225.840 E(ELEC)=-90.316 | | E(CDIH)=8.539 E(NOE )=211.255 E(PLAN)=10.111 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =78.532 grad(E)=2.631 E(BOND)=19.090 E(ANGL)=142.269 | | E(DIHE)=0.000 E(IMPR)=17.838 E(VDW )=-242.099 E(ELEC)=-94.261 | | E(CDIH)=6.669 E(NOE )=217.540 E(PLAN)=11.486 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =69.201 grad(E)=3.217 E(BOND)=17.386 E(ANGL)=137.198 | | E(DIHE)=0.000 E(IMPR)=17.209 E(VDW )=-241.577 E(ELEC)=-95.529 | | E(CDIH)=6.196 E(NOE )=216.912 E(PLAN)=11.407 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =61.116 grad(E)=2.943 E(BOND)=18.205 E(ANGL)=134.129 | | E(DIHE)=0.000 E(IMPR)=17.752 E(VDW )=-242.769 E(ELEC)=-100.226 | | E(CDIH)=6.109 E(NOE )=216.771 E(PLAN)=11.145 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =55.999 grad(E)=2.212 E(BOND)=16.996 E(ANGL)=132.864 | | E(DIHE)=0.000 E(IMPR)=17.702 E(VDW )=-239.245 E(ELEC)=-103.723 | | E(CDIH)=5.975 E(NOE )=214.311 E(PLAN)=11.119 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =51.806 grad(E)=1.675 E(BOND)=17.885 E(ANGL)=132.592 | | E(DIHE)=0.000 E(IMPR)=17.225 E(VDW )=-238.278 E(ELEC)=-107.831 | | E(CDIH)=7.137 E(NOE )=211.724 E(PLAN)=11.353 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =48.292 grad(E)=1.762 E(BOND)=17.352 E(ANGL)=130.082 | | E(DIHE)=0.000 E(IMPR)=16.992 E(VDW )=-237.148 E(ELEC)=-111.448 | | E(CDIH)=8.002 E(NOE )=213.147 E(PLAN)=11.315 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 64914 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =44.656 grad(E)=1.678 E(BOND)=18.140 E(ANGL)=129.334 | | E(DIHE)=0.000 E(IMPR)=16.874 E(VDW )=-235.857 E(ELEC)=-115.963 | | E(CDIH)=7.025 E(NOE )=213.702 E(PLAN)=11.401 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Constant temperature SA X-PLOR> X-PLOR>vector do (fbeta=100) (all) ! Coupling to heat bath. SELRPN: 677 atoms have been selected out of 677 X-PLOR>dynamics verlet DYNAmics> iasvel=maxwell DYNAmics> firsttemperature=$t DYNAmics> tbath=$t DYNAmics> tcoup=true DYNAmics> nstep=$steps DYNAmics> timestep=$timestep DYNAmics> nprint=250 DYNAmics> iprfrq=2500 DYNAmics> trajectory=refine.tra DYNAmics> nsavc=200 ! Save trajectory to file. DYNAmics>end ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.tra opened. DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 0.162641899E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.05120 0.01489 -0.00913 velocity [A/ps] : -0.00835 -0.12096 0.27753 ang. mom. [amu A/ps] : -6223.39854 -31803.60584 28640.86580 kin. ener. [Kcal/mol] : 0.73933 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.05120 0.01489 -0.00913 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)=660.266 E(kin)=615.610 temperature=305.061 | | Etotal =44.656 grad(E)=1.678 E(BOND)=18.140 E(ANGL)=129.334 | | E(DIHE)=0.000 E(IMPR)=16.874 E(VDW )=-235.857 E(ELEC)=-115.963 | | E(CDIH)=7.025 E(NOE )=213.702 E(PLAN)=11.401 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 64883 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 64837 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 64813 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart NBONDS: found 64828 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 64848 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64875 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 64892 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64855 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 64936 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 -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.49 A apart NBONDS: found 64964 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64965 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=1238.740 E(kin)=595.779 temperature=295.234 | | Etotal =642.960 grad(E)=65.114 E(BOND)=219.938 E(ANGL)=407.697 | | E(DIHE)=0.000 E(IMPR)=98.096 E(VDW )=-222.000 E(ELEC)=-119.584 | | E(CDIH)=10.893 E(NOE )=227.376 E(PLAN)=20.545 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65055 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64997 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65031 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65016 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64990 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 64984 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65024 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65041 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -10 -CYT -HO2'" and "A -13 -ADE -H62 " only 1.47 A apart NBONDS: found 65051 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65016 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -10 -CYT -HO2'" and "A -13 -ADE -H62 " only 1.45 A apart NBONDS: found 64919 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64857 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=1229.438 E(kin)=597.630 temperature=296.151 | | Etotal =631.808 grad(E)=64.646 E(BOND)=213.316 E(ANGL)=397.042 | | E(DIHE)=0.000 E(IMPR)=96.548 E(VDW )=-217.343 E(ELEC)=-120.395 | | E(CDIH)=13.203 E(NOE )=229.618 E(PLAN)=19.818 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64856 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64877 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64873 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64841 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 64811 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64793 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 64801 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64777 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64780 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64759 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64751 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=1201.410 E(kin)=609.423 temperature=301.995 | | Etotal =591.987 grad(E)=62.846 E(BOND)=212.086 E(ANGL)=377.715 | | E(DIHE)=0.000 E(IMPR)=77.672 E(VDW )=-219.956 E(ELEC)=-127.389 | | E(CDIH)=11.582 E(NOE )=243.020 E(PLAN)=17.259 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -10 -CYT -HO2'" 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 64741 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64768 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.18 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64746 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64760 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64716 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64710 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64652 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64612 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64555 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64518 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 64523 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64533 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64489 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64490 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=1217.060 E(kin)=609.687 temperature=302.126 | | Etotal =607.373 grad(E)=65.815 E(BOND)=206.996 E(ANGL)=402.952 | | E(DIHE)=0.000 E(IMPR)=80.925 E(VDW )=-223.769 E(ELEC)=-124.397 | | E(CDIH)=7.516 E(NOE )=242.978 E(PLAN)=14.171 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64498 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64529 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64576 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64601 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64581 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64520 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64507 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64497 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64497 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64515 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64510 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64474 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.44 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64505 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64496 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64550 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=1205.449 E(kin)=590.740 temperature=292.737 | | Etotal =614.708 grad(E)=61.943 E(BOND)=218.553 E(ANGL)=390.134 | | E(DIHE)=0.000 E(IMPR)=90.316 E(VDW )=-226.157 E(ELEC)=-141.469 | | E(CDIH)=7.265 E(NOE )=262.580 E(PLAN)=13.487 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64565 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64569 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64594 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64610 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64632 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64610 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64579 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64581 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 64584 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64615 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64630 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=1198.284 E(kin)=596.865 temperature=295.772 | | Etotal =601.419 grad(E)=63.167 E(BOND)=215.507 E(ANGL)=397.260 | | E(DIHE)=0.000 E(IMPR)=96.105 E(VDW )=-227.027 E(ELEC)=-149.418 | | E(CDIH)=9.929 E(NOE )=242.048 E(PLAN)=17.015 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64672 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64647 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64681 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64712 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64695 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64737 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64771 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64819 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64844 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=1211.290 E(kin)=610.027 temperature=302.294 | | Etotal =601.263 grad(E)=63.099 E(BOND)=206.811 E(ANGL)=409.177 | | E(DIHE)=0.000 E(IMPR)=85.605 E(VDW )=-234.107 E(ELEC)=-140.817 | | E(CDIH)=10.762 E(NOE )=248.446 E(PLAN)=15.386 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 64888 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 64936 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 64967 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65004 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65024 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65054 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65013 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64967 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64946 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64947 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=1221.556 E(kin)=580.762 temperature=287.792 | | Etotal =640.793 grad(E)=65.057 E(BOND)=211.223 E(ANGL)=423.558 | | E(DIHE)=0.000 E(IMPR)=106.833 E(VDW )=-240.098 E(ELEC)=-130.046 | | E(CDIH)=17.949 E(NOE )=235.907 E(PLAN)=15.468 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64931 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64997 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65017 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64989 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65093 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65128 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65147 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=1230.014 E(kin)=615.349 temperature=304.931 | | Etotal =614.665 grad(E)=63.232 E(BOND)=218.878 E(ANGL)=399.028 | | E(DIHE)=0.000 E(IMPR)=82.640 E(VDW )=-247.546 E(ELEC)=-130.562 | | E(CDIH)=12.230 E(NOE )=263.418 E(PLAN)=16.578 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65239 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65279 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65305 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65334 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65327 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65253 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65209 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65166 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -11 -ADE -H5''" only 1.42 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65131 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -11 -ADE -H5''" only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65087 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65092 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=1216.977 E(kin)=581.073 temperature=287.946 | | Etotal =635.904 grad(E)=65.177 E(BOND)=202.659 E(ANGL)=428.250 | | E(DIHE)=0.000 E(IMPR)=90.706 E(VDW )=-246.203 E(ELEC)=-134.973 | | E(CDIH)=9.762 E(NOE )=264.411 E(PLAN)=21.293 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1215.687 E(kin)=603.365 temperature=298.992 | | Etotal =612.323 grad(E)=63.950 E(BOND)=211.013 E(ANGL)=394.459 | | E(DIHE)=0.000 E(IMPR)=90.158 E(VDW )=-229.006 E(ELEC)=-131.038 | | E(CDIH)=9.398 E(NOE )=250.674 E(PLAN)=16.666 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=40.380 E(kin)=21.835 temperature=10.820 | | Etotal =29.697 grad(E)=2.017 E(BOND)=12.220 E(ANGL)=18.813 | | E(DIHE)=0.000 E(IMPR)=7.439 E(VDW )=8.776 E(ELEC)=10.502 | | E(CDIH)=3.358 E(NOE )=11.218 E(PLAN)=2.934 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65092 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65099 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65098 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65100 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65086 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65060 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65068 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65078 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65115 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65130 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65119 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65176 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65213 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65180 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=1210.340 E(kin)=615.370 temperature=304.942 | | Etotal =594.970 grad(E)=63.969 E(BOND)=197.663 E(ANGL)=404.307 | | E(DIHE)=0.000 E(IMPR)=98.647 E(VDW )=-244.206 E(ELEC)=-139.087 | | E(CDIH)=4.491 E(NOE )=254.445 E(PLAN)=18.710 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65196 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65218 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65285 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65332 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 65403 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 65413 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.17 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65448 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 65503 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65525 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65521 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65559 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65530 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 65533 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65494 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65445 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=1200.810 E(kin)=623.747 temperature=309.093 | | Etotal =577.064 grad(E)=63.532 E(BOND)=198.508 E(ANGL)=379.558 | | E(DIHE)=0.000 E(IMPR)=89.069 E(VDW )=-227.687 E(ELEC)=-136.347 | | E(CDIH)=13.064 E(NOE )=244.430 E(PLAN)=16.470 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 65330 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart NBONDS: found 65282 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65182 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart NBONDS: found 65123 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65087 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65063 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65022 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65022 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65051 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65034 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=1235.861 E(kin)=619.290 temperature=306.884 | | Etotal =616.571 grad(E)=63.098 E(BOND)=222.938 E(ANGL)=366.507 | | E(DIHE)=0.000 E(IMPR)=95.690 E(VDW )=-216.463 E(ELEC)=-135.778 | | E(CDIH)=7.540 E(NOE )=257.319 E(PLAN)=18.818 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65050 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64984 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64963 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64935 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64879 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64830 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64777 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64850 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64884 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=1203.331 E(kin)=619.509 temperature=306.993 | | Etotal =583.821 grad(E)=65.436 E(BOND)=193.207 E(ANGL)=395.467 | | E(DIHE)=0.000 E(IMPR)=79.167 E(VDW )=-219.907 E(ELEC)=-134.360 | | E(CDIH)=4.640 E(NOE )=249.692 E(PLAN)=15.915 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 64913 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64920 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.48 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64916 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64980 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64928 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65020 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65069 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=1202.557 E(kin)=609.414 temperature=301.990 | | Etotal =593.143 grad(E)=63.248 E(BOND)=210.084 E(ANGL)=384.547 | | E(DIHE)=0.000 E(IMPR)=87.945 E(VDW )=-226.798 E(ELEC)=-144.947 | | E(CDIH)=15.461 E(NOE )=246.909 E(PLAN)=19.942 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65062 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65002 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65132 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65206 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65258 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65390 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=1216.146 E(kin)=588.283 temperature=291.519 | | Etotal =627.863 grad(E)=65.332 E(BOND)=224.109 E(ANGL)=403.096 | | E(DIHE)=0.000 E(IMPR)=101.093 E(VDW )=-244.308 E(ELEC)=-132.582 | | E(CDIH)=5.872 E(NOE )=254.391 E(PLAN)=16.192 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65535 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 65677 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.50 A apart NBONDS: found 65837 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65817 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65734 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65767 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=1249.829 E(kin)=604.816 temperature=299.712 | | Etotal =645.013 grad(E)=65.945 E(BOND)=215.386 E(ANGL)=428.475 | | E(DIHE)=0.000 E(IMPR)=83.338 E(VDW )=-229.038 E(ELEC)=-126.302 | | E(CDIH)=10.599 E(NOE )=248.886 E(PLAN)=13.669 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65889 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66038 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66158 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66177 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66181 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 66148 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 66142 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=1228.130 E(kin)=596.595 temperature=295.638 | | Etotal =631.535 grad(E)=67.792 E(BOND)=216.004 E(ANGL)=402.413 | | E(DIHE)=0.000 E(IMPR)=96.432 E(VDW )=-214.412 E(ELEC)=-136.103 | | E(CDIH)=8.145 E(NOE )=246.172 E(PLAN)=12.883 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 66121 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66010 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -10 -CYT -O2' " and "A -13 -ADE -H62 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65940 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 65843 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65734 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65662 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65598 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=1221.809 E(kin)=604.974 temperature=299.790 | | Etotal =616.835 grad(E)=64.940 E(BOND)=197.207 E(ANGL)=411.012 | | E(DIHE)=0.000 E(IMPR)=105.088 E(VDW )=-221.266 E(ELEC)=-142.580 | | E(CDIH)=9.123 E(NOE )=242.255 E(PLAN)=15.995 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65577 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65582 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65583 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.18 A apart NBONDS: found 65582 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65521 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65536 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 65522 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65513 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=1216.855 E(kin)=605.328 temperature=299.965 | | Etotal =611.527 grad(E)=66.222 E(BOND)=208.739 E(ANGL)=399.148 | | E(DIHE)=0.000 E(IMPR)=96.669 E(VDW )=-240.684 E(ELEC)=-136.521 | | E(CDIH)=5.828 E(NOE )=261.962 E(PLAN)=16.385 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1218.436 E(kin)=605.494 temperature=300.048 | | Etotal =612.941 grad(E)=65.024 E(BOND)=210.348 E(ANGL)=395.601 | | E(DIHE)=0.000 E(IMPR)=94.571 E(VDW )=-227.255 E(ELEC)=-138.013 | | E(CDIH)=9.099 E(NOE )=252.328 E(PLAN)=16.262 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=14.364 E(kin)=12.401 temperature=6.145 | | Etotal =18.617 grad(E)=1.520 E(BOND)=10.624 E(ANGL)=13.316 | | E(DIHE)=0.000 E(IMPR)=6.528 E(VDW )=9.328 E(ELEC)=5.515 | | E(CDIH)=3.217 E(NOE )=11.626 E(PLAN)=2.886 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=1217.061 E(kin)=604.429 temperature=299.520 | | Etotal =612.632 grad(E)=64.487 E(BOND)=210.681 E(ANGL)=395.030 | | E(DIHE)=0.000 E(IMPR)=92.364 E(VDW )=-228.130 E(ELEC)=-134.526 | | E(CDIH)=9.248 E(NOE )=251.501 E(PLAN)=16.464 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=30.337 E(kin)=17.788 temperature=8.815 | | Etotal =24.786 grad(E)=1.865 E(BOND)=11.455 E(ANGL)=16.308 | | E(DIHE)=0.000 E(IMPR)=7.338 E(VDW )=9.098 E(ELEC)=9.084 | | E(CDIH)=3.291 E(NOE )=11.454 E(PLAN)=2.917 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65486 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65484 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65412 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.49 A apart NBONDS: found 65297 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65278 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65249 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65322 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65322 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65398 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=1201.302 E(kin)=600.116 temperature=297.382 | | Etotal =601.186 grad(E)=66.999 E(BOND)=210.551 E(ANGL)=393.040 | | E(DIHE)=0.000 E(IMPR)=99.337 E(VDW )=-236.401 E(ELEC)=-140.789 | | E(CDIH)=9.470 E(NOE )=249.876 E(PLAN)=16.102 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65439 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65498 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.42 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65618 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65675 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.49 A apart NBONDS: found 65748 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65767 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65826 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65832 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=1209.884 E(kin)=589.432 temperature=292.088 | | Etotal =620.452 grad(E)=65.745 E(BOND)=221.655 E(ANGL)=392.495 | | E(DIHE)=0.000 E(IMPR)=93.487 E(VDW )=-222.547 E(ELEC)=-135.715 | | E(CDIH)=8.445 E(NOE )=248.734 E(PLAN)=13.898 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 65751 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65724 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65738 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65712 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65801 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65763 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65784 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65782 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65768 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=1220.582 E(kin)=591.135 temperature=292.932 | | Etotal =629.448 grad(E)=66.173 E(BOND)=236.426 E(ANGL)=399.418 | | E(DIHE)=0.000 E(IMPR)=104.655 E(VDW )=-235.717 E(ELEC)=-135.389 | | E(CDIH)=8.866 E(NOE )=236.393 E(PLAN)=14.795 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65758 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65746 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65695 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65708 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65598 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65620 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 65553 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65519 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65505 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=1217.843 E(kin)=607.772 temperature=301.176 | | Etotal =610.071 grad(E)=65.050 E(BOND)=213.188 E(ANGL)=387.730 | | E(DIHE)=0.000 E(IMPR)=95.919 E(VDW )=-239.190 E(ELEC)=-131.964 | | E(CDIH)=9.900 E(NOE )=257.248 E(PLAN)=17.241 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65472 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65462 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65437 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65437 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 65472 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65491 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65500 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65536 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 65544 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=1221.245 E(kin)=613.996 temperature=304.261 | | Etotal =607.249 grad(E)=63.847 E(BOND)=216.480 E(ANGL)=395.372 | | E(DIHE)=0.000 E(IMPR)=103.954 E(VDW )=-235.815 E(ELEC)=-146.074 | | E(CDIH)=6.049 E(NOE )=251.545 E(PLAN)=15.738 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65550 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65529 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65478 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65418 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65385 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65332 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65286 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65292 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65253 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65202 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65151 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=1210.113 E(kin)=608.578 temperature=301.576 | | Etotal =601.535 grad(E)=65.743 E(BOND)=218.534 E(ANGL)=392.370 | | E(DIHE)=0.000 E(IMPR)=99.443 E(VDW )=-233.675 E(ELEC)=-141.307 | | E(CDIH)=8.875 E(NOE )=241.548 E(PLAN)=15.748 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65152 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65150 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65138 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65094 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65107 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 65123 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65145 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65146 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=1219.479 E(kin)=607.608 temperature=301.095 | | Etotal =611.871 grad(E)=67.675 E(BOND)=226.373 E(ANGL)=381.301 | | E(DIHE)=0.000 E(IMPR)=92.213 E(VDW )=-228.471 E(ELEC)=-145.715 | | E(CDIH)=13.456 E(NOE )=255.871 E(PLAN)=16.844 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65133 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65113 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64998 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64809 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 64583 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=1205.304 E(kin)=614.596 temperature=304.558 | | Etotal =590.708 grad(E)=64.547 E(BOND)=215.129 E(ANGL)=375.774 | | E(DIHE)=0.000 E(IMPR)=100.039 E(VDW )=-227.981 E(ELEC)=-144.026 | | E(CDIH)=6.636 E(NOE )=246.919 E(PLAN)=18.219 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64537 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64457 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64442 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 64434 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.18 A apart NBONDS: found 64428 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 64452 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64475 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=1220.289 E(kin)=597.337 temperature=296.006 | | Etotal =622.951 grad(E)=69.270 E(BOND)=218.642 E(ANGL)=388.463 | | E(DIHE)=0.000 E(IMPR)=102.950 E(VDW )=-221.401 E(ELEC)=-143.128 | | E(CDIH)=10.876 E(NOE )=249.888 E(PLAN)=16.661 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64497 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64534 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64459 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 64479 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 64472 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64449 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=1233.762 E(kin)=611.857 temperature=303.201 | | Etotal =621.905 grad(E)=67.520 E(BOND)=207.225 E(ANGL)=410.222 | | E(DIHE)=0.000 E(IMPR)=92.694 E(VDW )=-224.647 E(ELEC)=-141.629 | | E(CDIH)=11.129 E(NOE )=249.475 E(PLAN)=17.435 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1216.770 E(kin)=605.394 temperature=299.998 | | Etotal =611.376 grad(E)=65.574 E(BOND)=215.394 E(ANGL)=396.493 | | E(DIHE)=0.000 E(IMPR)=96.583 E(VDW )=-232.614 E(ELEC)=-140.674 | | E(CDIH)=9.167 E(NOE )=250.743 E(PLAN)=16.284 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.146 E(kin)=11.907 temperature=5.900 | | Etotal =15.263 grad(E)=1.507 E(BOND)=10.782 E(ANGL)=13.392 | | E(DIHE)=0.000 E(IMPR)=6.824 E(VDW )=8.045 E(ELEC)=5.296 | | E(CDIH)=2.969 E(NOE )=9.191 E(PLAN)=1.803 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=1216.964 E(kin)=604.751 temperature=299.680 | | Etotal =612.213 grad(E)=64.849 E(BOND)=212.252 E(ANGL)=395.518 | | E(DIHE)=0.000 E(IMPR)=93.771 E(VDW )=-229.625 E(ELEC)=-136.575 | | E(CDIH)=9.221 E(NOE )=251.248 E(PLAN)=16.404 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=25.454 E(kin)=16.075 temperature=7.966 | | Etotal =22.081 grad(E)=1.827 E(BOND)=11.453 E(ANGL)=15.413 | | E(DIHE)=0.000 E(IMPR)=7.441 E(VDW )=9.013 E(ELEC)=8.530 | | E(CDIH)=3.188 E(NOE )=10.759 E(PLAN)=2.601 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64460 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64485 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64543 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.50 A apart NBONDS: found 64558 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 64568 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64667 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64754 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 64803 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64844 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64887 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64944 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=1201.700 E(kin)=582.853 temperature=288.828 | | Etotal =618.847 grad(E)=67.403 E(BOND)=213.811 E(ANGL)=396.525 | | E(DIHE)=0.000 E(IMPR)=113.266 E(VDW )=-225.773 E(ELEC)=-138.931 | | E(CDIH)=6.930 E(NOE )=235.619 E(PLAN)=17.400 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64948 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64944 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64968 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 64980 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65050 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65031 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 64999 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64943 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 64909 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 64922 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 64914 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=1231.977 E(kin)=618.754 temperature=306.619 | | Etotal =613.224 grad(E)=65.822 E(BOND)=207.293 E(ANGL)=394.833 | | E(DIHE)=0.000 E(IMPR)=83.965 E(VDW )=-223.693 E(ELEC)=-138.360 | | E(CDIH)=8.161 E(NOE )=262.455 E(PLAN)=18.570 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 64942 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -12 -URI -H6 " and "A -13 -ADE -H61 " only 1.43 A apart NBONDS: found 64916 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64954 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64996 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65041 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65107 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65150 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65249 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65280 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65314 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=1218.495 E(kin)=618.018 temperature=306.254 | | Etotal =600.477 grad(E)=65.476 E(BOND)=237.059 E(ANGL)=362.696 | | E(DIHE)=0.000 E(IMPR)=88.807 E(VDW )=-234.847 E(ELEC)=-127.444 | | E(CDIH)=15.095 E(NOE )=246.003 E(PLAN)=13.110 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65397 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65511 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65570 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65603 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65576 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65509 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65479 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65409 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65365 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=1188.604 E(kin)=603.921 temperature=299.268 | | Etotal =584.683 grad(E)=65.203 E(BOND)=216.334 E(ANGL)=376.984 | | E(DIHE)=0.000 E(IMPR)=91.623 E(VDW )=-217.112 E(ELEC)=-142.052 | | E(CDIH)=5.066 E(NOE )=240.731 E(PLAN)=13.109 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65274 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65259 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65209 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65234 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 65255 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 65272 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart NBONDS: found 65362 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 65388 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=1223.473 E(kin)=605.824 temperature=300.211 | | Etotal =617.650 grad(E)=67.895 E(BOND)=223.101 E(ANGL)=378.203 | | E(DIHE)=0.000 E(IMPR)=97.410 E(VDW )=-215.080 E(ELEC)=-154.037 | | E(CDIH)=12.313 E(NOE )=262.403 E(PLAN)=13.337 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65340 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65378 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65380 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65395 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65399 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 65383 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65419 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65447 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65520 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=1211.549 E(kin)=609.128 temperature=301.849 | | Etotal =602.421 grad(E)=65.678 E(BOND)=214.521 E(ANGL)=404.904 | | E(DIHE)=0.000 E(IMPR)=86.464 E(VDW )=-210.195 E(ELEC)=-153.536 | | E(CDIH)=10.567 E(NOE )=229.008 E(PLAN)=20.689 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65511 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65610 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65690 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65702 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65791 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65881 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=1218.379 E(kin)=617.400 temperature=305.948 | | Etotal =600.978 grad(E)=66.440 E(BOND)=227.479 E(ANGL)=393.612 | | E(DIHE)=0.000 E(IMPR)=94.682 E(VDW )=-238.890 E(ELEC)=-145.447 | | E(CDIH)=7.315 E(NOE )=242.855 E(PLAN)=19.373 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65966 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65994 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66071 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -10 -CYT -H4' " and "A -11 -ADE -O5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66092 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66079 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66027 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=1209.081 E(kin)=601.753 temperature=298.194 | | Etotal =607.328 grad(E)=67.618 E(BOND)=229.379 E(ANGL)=404.137 | | E(DIHE)=0.000 E(IMPR)=89.304 E(VDW )=-240.617 E(ELEC)=-143.459 | | E(CDIH)=6.572 E(NOE )=245.687 E(PLAN)=16.326 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65972 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65934 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65932 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65912 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65897 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65930 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65819 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=1216.505 E(kin)=631.666 temperature=313.017 | | Etotal =584.839 grad(E)=65.384 E(BOND)=219.443 E(ANGL)=385.686 | | E(DIHE)=0.000 E(IMPR)=88.501 E(VDW )=-233.892 E(ELEC)=-144.726 | | E(CDIH)=13.219 E(NOE )=241.137 E(PLAN)=15.472 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 65704 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 65643 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 65684 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 65595 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65563 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=1219.787 E(kin)=570.996 temperature=282.953 | | Etotal =648.791 grad(E)=70.073 E(BOND)=230.279 E(ANGL)=414.610 | | E(DIHE)=0.000 E(IMPR)=107.140 E(VDW )=-245.355 E(ELEC)=-142.690 | | E(CDIH)=11.462 E(NOE )=258.569 E(PLAN)=14.776 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1215.364 E(kin)=605.526 temperature=300.063 | | Etotal =609.839 grad(E)=66.402 E(BOND)=221.989 E(ANGL)=393.122 | | E(DIHE)=0.000 E(IMPR)=94.530 E(VDW )=-229.969 E(ELEC)=-142.935 | | E(CDIH)=8.809 E(NOE )=248.702 E(PLAN)=15.590 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.233 E(kin)=12.302 temperature=6.096 | | Etotal =14.933 grad(E)=1.453 E(BOND)=11.079 E(ANGL)=12.208 | | E(DIHE)=0.000 E(IMPR)=6.659 E(VDW )=8.610 E(ELEC)=7.100 | | E(CDIH)=3.009 E(NOE )=9.435 E(PLAN)=2.005 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=1216.564 E(kin)=604.945 temperature=299.776 | | Etotal =611.620 grad(E)=65.238 E(BOND)=214.686 E(ANGL)=394.919 | | E(DIHE)=0.000 E(IMPR)=93.961 E(VDW )=-229.711 E(ELEC)=-138.165 | | E(CDIH)=9.118 E(NOE )=250.612 E(PLAN)=16.200 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=22.532 E(kin)=15.223 temperature=7.544 | | Etotal =20.554 grad(E)=1.866 E(BOND)=12.118 E(ANGL)=14.714 | | E(DIHE)=0.000 E(IMPR)=7.261 E(VDW )=8.915 E(ELEC)=8.646 | | E(CDIH)=3.149 E(NOE )=10.502 E(PLAN)=2.490 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65403 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65407 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65420 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65461 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65520 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65607 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 65695 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=1227.501 E(kin)=605.569 temperature=300.085 | | Etotal =621.932 grad(E)=66.707 E(BOND)=222.660 E(ANGL)=418.170 | | E(DIHE)=0.000 E(IMPR)=100.236 E(VDW )=-230.777 E(ELEC)=-145.861 | | E(CDIH)=5.806 E(NOE )=235.563 E(PLAN)=16.135 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65826 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65929 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65985 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 66020 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65983 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=1225.557 E(kin)=620.847 temperature=307.656 | | Etotal =604.710 grad(E)=67.134 E(BOND)=234.489 E(ANGL)=386.879 | | E(DIHE)=0.000 E(IMPR)=92.667 E(VDW )=-229.957 E(ELEC)=-136.460 | | E(CDIH)=11.126 E(NOE )=230.857 E(PLAN)=15.108 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 65878 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65707 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65522 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65349 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65208 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65037 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64974 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=1223.679 E(kin)=637.147 temperature=315.733 | | Etotal =586.533 grad(E)=65.058 E(BOND)=223.318 E(ANGL)=376.566 | | E(DIHE)=0.000 E(IMPR)=90.056 E(VDW )=-232.003 E(ELEC)=-127.772 | | E(CDIH)=7.352 E(NOE )=236.809 E(PLAN)=12.206 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64946 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64928 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64931 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64839 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64835 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64831 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64817 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 64766 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=1218.693 E(kin)=600.338 temperature=297.493 | | Etotal =618.355 grad(E)=66.376 E(BOND)=219.248 E(ANGL)=414.622 | | E(DIHE)=0.000 E(IMPR)=90.847 E(VDW )=-220.057 E(ELEC)=-148.204 | | E(CDIH)=8.937 E(NOE )=236.821 E(PLAN)=16.141 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64696 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64573 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64520 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64401 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64351 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64258 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64216 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64155 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=1219.337 E(kin)=573.998 temperature=284.440 | | Etotal =645.338 grad(E)=66.902 E(BOND)=223.336 E(ANGL)=419.810 | | E(DIHE)=0.000 E(IMPR)=98.247 E(VDW )=-215.747 E(ELEC)=-142.434 | | E(CDIH)=10.422 E(NOE )=235.867 E(PLAN)=15.837 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.18 A apart NBONDS: found 64148 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 64090 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64046 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64000 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64062 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64097 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64174 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64217 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64228 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=1226.358 E(kin)=598.664 temperature=296.663 | | Etotal =627.694 grad(E)=67.185 E(BOND)=225.431 E(ANGL)=397.798 | | E(DIHE)=0.000 E(IMPR)=103.901 E(VDW )=-224.698 E(ELEC)=-145.567 | | E(CDIH)=13.453 E(NOE )=241.495 E(PLAN)=15.882 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64232 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 64252 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64313 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64316 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64293 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 64326 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64336 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64269 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64270 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=1219.613 E(kin)=606.432 temperature=300.513 | | Etotal =613.181 grad(E)=67.067 E(BOND)=224.657 E(ANGL)=397.086 | | E(DIHE)=0.000 E(IMPR)=88.397 E(VDW )=-220.170 E(ELEC)=-150.161 | | E(CDIH)=8.935 E(NOE )=248.819 E(PLAN)=15.619 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64239 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64193 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64141 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64120 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64079 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64052 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64004 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 64011 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=1226.310 E(kin)=608.956 temperature=301.764 | | Etotal =617.354 grad(E)=67.884 E(BOND)=223.222 E(ANGL)=390.097 | | E(DIHE)=0.000 E(IMPR)=98.378 E(VDW )=-218.118 E(ELEC)=-152.192 | | E(CDIH)=16.611 E(NOE )=243.455 E(PLAN)=15.900 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 63996 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64037 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64080 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 64111 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64186 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64262 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart NBONDS: found 64345 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart NBONDS: found 64349 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64363 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=1227.562 E(kin)=611.022 temperature=302.787 | | Etotal =616.540 grad(E)=65.784 E(BOND)=220.091 E(ANGL)=417.005 | | E(DIHE)=0.000 E(IMPR)=85.146 E(VDW )=-224.919 E(ELEC)=-142.541 | | E(CDIH)=7.211 E(NOE )=234.895 E(PLAN)=19.652 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart NBONDS: found 64404 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64414 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64390 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64405 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64428 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64365 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64280 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 64288 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64263 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=1217.691 E(kin)=613.113 temperature=303.823 | | Etotal =604.578 grad(E)=65.585 E(BOND)=213.246 E(ANGL)=402.697 | | E(DIHE)=0.000 E(IMPR)=99.417 E(VDW )=-228.976 E(ELEC)=-144.818 | | E(CDIH)=10.051 E(NOE )=236.062 E(PLAN)=16.900 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1220.419 E(kin)=605.511 temperature=300.056 | | Etotal =614.907 grad(E)=67.399 E(BOND)=224.633 E(ANGL)=400.204 | | E(DIHE)=0.000 E(IMPR)=95.399 E(VDW )=-229.922 E(ELEC)=-143.529 | | E(CDIH)=9.055 E(NOE )=243.449 E(PLAN)=15.618 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.865 E(kin)=12.688 temperature=6.287 | | Etotal =14.503 grad(E)=1.487 E(BOND)=10.380 E(ANGL)=13.284 | | E(DIHE)=0.000 E(IMPR)=6.556 E(VDW )=8.584 E(ELEC)=6.693 | | E(CDIH)=2.966 E(NOE )=9.199 E(PLAN)=2.170 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=1217.335 E(kin)=605.058 temperature=299.832 | | Etotal =612.277 grad(E)=65.670 E(BOND)=216.675 E(ANGL)=395.976 | | E(DIHE)=0.000 E(IMPR)=94.248 E(VDW )=-229.753 E(ELEC)=-139.238 | | E(CDIH)=9.106 E(NOE )=249.179 E(PLAN)=16.084 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=20.516 E(kin)=14.753 temperature=7.311 | | Etotal =19.539 grad(E)=1.994 E(BOND)=12.444 E(ANGL)=14.593 | | E(DIHE)=0.000 E(IMPR)=7.149 E(VDW )=8.850 E(ELEC)=8.565 | | E(CDIH)=3.113 E(NOE )=10.647 E(PLAN)=2.441 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64306 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64358 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 64420 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64446 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 64479 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64568 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64670 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64701 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64850 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=1208.048 E(kin)=588.176 temperature=291.466 | | Etotal =619.872 grad(E)=66.546 E(BOND)=231.369 E(ANGL)=404.159 | | E(DIHE)=0.000 E(IMPR)=93.373 E(VDW )=-253.294 E(ELEC)=-146.133 | | E(CDIH)=9.645 E(NOE )=267.320 E(PLAN)=13.433 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart NBONDS: found 65002 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65065 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65112 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65156 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65177 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65228 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65247 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65265 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=1217.381 E(kin)=592.705 temperature=293.710 | | Etotal =624.676 grad(E)=67.786 E(BOND)=220.708 E(ANGL)=418.351 | | E(DIHE)=0.000 E(IMPR)=101.048 E(VDW )=-236.907 E(ELEC)=-148.291 | | E(CDIH)=5.364 E(NOE )=249.623 E(PLAN)=14.781 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.17 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 65269 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65318 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65303 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65357 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65355 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65417 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65479 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=1195.246 E(kin)=601.463 temperature=298.050 | | Etotal =593.783 grad(E)=64.980 E(BOND)=214.758 E(ANGL)=409.895 | | E(DIHE)=0.000 E(IMPR)=96.199 E(VDW )=-233.788 E(ELEC)=-157.775 | | E(CDIH)=7.081 E(NOE )=244.268 E(PLAN)=13.146 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65442 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65414 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65451 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65386 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65384 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65489 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65559 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=1206.381 E(kin)=617.525 temperature=306.010 | | Etotal =588.855 grad(E)=64.971 E(BOND)=206.424 E(ANGL)=397.919 | | E(DIHE)=0.000 E(IMPR)=93.867 E(VDW )=-236.068 E(ELEC)=-151.470 | | E(CDIH)=8.472 E(NOE )=255.487 E(PLAN)=14.224 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65560 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65543 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65539 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65598 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65627 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65691 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=1214.474 E(kin)=591.437 temperature=293.082 | | Etotal =623.036 grad(E)=65.229 E(BOND)=230.464 E(ANGL)=402.939 | | E(DIHE)=0.000 E(IMPR)=93.871 E(VDW )=-230.118 E(ELEC)=-154.995 | | E(CDIH)=6.641 E(NOE )=256.920 E(PLAN)=17.315 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65703 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65623 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65458 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65455 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65507 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65492 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=1223.046 E(kin)=595.457 temperature=295.074 | | Etotal =627.589 grad(E)=67.189 E(BOND)=230.657 E(ANGL)=406.664 | | E(DIHE)=0.000 E(IMPR)=84.762 E(VDW )=-239.675 E(ELEC)=-140.977 | | E(CDIH)=15.036 E(NOE )=255.712 E(PLAN)=15.409 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 65528 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65621 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65785 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65791 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 65791 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65793 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=1215.669 E(kin)=610.758 temperature=302.656 | | Etotal =604.910 grad(E)=68.321 E(BOND)=227.823 E(ANGL)=404.523 | | E(DIHE)=0.000 E(IMPR)=94.208 E(VDW )=-226.500 E(ELEC)=-147.050 | | E(CDIH)=6.273 E(NOE )=231.248 E(PLAN)=14.385 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65868 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65843 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65808 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 65751 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65694 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65666 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65684 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=1209.655 E(kin)=605.242 temperature=299.923 | | Etotal =604.413 grad(E)=64.043 E(BOND)=209.900 E(ANGL)=430.917 | | E(DIHE)=0.000 E(IMPR)=93.711 E(VDW )=-247.597 E(ELEC)=-146.057 | | E(CDIH)=5.540 E(NOE )=243.021 E(PLAN)=14.978 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65703 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65804 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65846 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65791 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=1219.747 E(kin)=595.216 temperature=294.954 | | Etotal =624.531 grad(E)=65.382 E(BOND)=215.133 E(ANGL)=425.509 | | E(DIHE)=0.000 E(IMPR)=101.115 E(VDW )=-241.581 E(ELEC)=-140.608 | | E(CDIH)=4.854 E(NOE )=248.769 E(PLAN)=11.341 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65709 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65587 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65519 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65475 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65460 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65477 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65440 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=1217.684 E(kin)=609.014 temperature=301.792 | | Etotal =608.670 grad(E)=64.866 E(BOND)=234.482 E(ANGL)=397.577 | | E(DIHE)=0.000 E(IMPR)=96.317 E(VDW )=-243.070 E(ELEC)=-140.003 | | E(CDIH)=4.707 E(NOE )=244.074 E(PLAN)=14.585 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1213.214 E(kin)=605.473 temperature=300.037 | | Etotal =607.741 grad(E)=66.122 E(BOND)=223.154 E(ANGL)=401.415 | | E(DIHE)=0.000 E(IMPR)=92.824 E(VDW )=-236.588 E(ELEC)=-147.436 | | E(CDIH)=8.267 E(NOE )=250.847 E(PLAN)=15.259 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.662 E(kin)=12.369 temperature=6.129 | | Etotal =15.223 grad(E)=1.328 E(BOND)=9.747 E(ANGL)=11.934 | | E(DIHE)=0.000 E(IMPR)=6.803 E(VDW )=7.120 E(ELEC)=5.980 | | E(CDIH)=2.716 E(NOE )=9.443 E(PLAN)=1.944 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=1216.648 E(kin)=605.127 temperature=299.866 | | Etotal =611.521 grad(E)=65.745 E(BOND)=217.755 E(ANGL)=396.883 | | E(DIHE)=0.000 E(IMPR)=94.011 E(VDW )=-230.892 E(ELEC)=-140.604 | | E(CDIH)=8.966 E(NOE )=249.457 E(PLAN)=15.946 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=19.201 E(kin)=14.384 temperature=7.128 | | Etotal =18.964 grad(E)=1.907 E(BOND)=12.276 E(ANGL)=14.329 | | E(DIHE)=0.000 E(IMPR)=7.112 E(VDW )=8.956 E(ELEC)=8.742 | | E(CDIH)=3.067 E(NOE )=10.474 E(PLAN)=2.385 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65365 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65393 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65388 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65398 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65416 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65404 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=1222.283 E(kin)=606.515 temperature=300.554 | | Etotal =615.768 grad(E)=66.413 E(BOND)=215.026 E(ANGL)=391.418 | | E(DIHE)=0.000 E(IMPR)=96.989 E(VDW )=-208.640 E(ELEC)=-152.058 | | E(CDIH)=5.006 E(NOE )=250.462 E(PLAN)=17.564 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65365 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65302 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65266 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 65218 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65256 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65278 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 65219 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=1213.220 E(kin)=602.871 temperature=298.748 | | Etotal =610.350 grad(E)=65.865 E(BOND)=232.230 E(ANGL)=398.227 | | E(DIHE)=0.000 E(IMPR)=89.041 E(VDW )=-230.428 E(ELEC)=-156.159 | | E(CDIH)=5.902 E(NOE )=254.584 E(PLAN)=16.952 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65167 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65123 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65127 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65131 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65018 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65022 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=1210.566 E(kin)=590.076 temperature=292.407 | | Etotal =620.490 grad(E)=66.426 E(BOND)=226.888 E(ANGL)=394.928 | | E(DIHE)=0.000 E(IMPR)=91.714 E(VDW )=-235.941 E(ELEC)=-146.563 | | E(CDIH)=17.331 E(NOE )=256.946 E(PLAN)=15.185 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart NBONDS: found 64957 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64930 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64872 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64934 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64913 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64872 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 64785 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=1215.959 E(kin)=596.655 temperature=295.667 | | Etotal =619.305 grad(E)=67.078 E(BOND)=225.884 E(ANGL)=417.185 | | E(DIHE)=0.000 E(IMPR)=92.307 E(VDW )=-225.376 E(ELEC)=-149.082 | | E(CDIH)=8.424 E(NOE )=235.241 E(PLAN)=14.722 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64783 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64781 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64794 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64705 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64676 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64714 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=1208.751 E(kin)=597.142 temperature=295.909 | | Etotal =611.609 grad(E)=65.350 E(BOND)=229.726 E(ANGL)=418.103 | | E(DIHE)=0.000 E(IMPR)=82.656 E(VDW )=-225.106 E(ELEC)=-153.589 | | E(CDIH)=5.844 E(NOE )=237.403 E(PLAN)=16.571 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64685 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64722 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64739 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 64679 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64718 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 64703 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=1229.651 E(kin)=623.586 temperature=309.013 | | Etotal =606.066 grad(E)=67.363 E(BOND)=224.685 E(ANGL)=399.584 | | E(DIHE)=0.000 E(IMPR)=92.986 E(VDW )=-229.265 E(ELEC)=-151.683 | | E(CDIH)=1.872 E(NOE )=247.178 E(PLAN)=20.708 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 64664 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64628 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64664 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64680 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64775 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 64819 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 64873 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=1202.238 E(kin)=607.285 temperature=300.935 | | Etotal =594.952 grad(E)=64.057 E(BOND)=220.240 E(ANGL)=377.159 | | E(DIHE)=0.000 E(IMPR)=85.436 E(VDW )=-227.200 E(ELEC)=-148.614 | | E(CDIH)=12.001 E(NOE )=261.622 E(PLAN)=14.309 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 64937 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64978 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64872 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64829 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64852 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=1226.510 E(kin)=622.138 temperature=308.296 | | Etotal =604.372 grad(E)=65.326 E(BOND)=221.346 E(ANGL)=385.063 | | E(DIHE)=0.000 E(IMPR)=91.331 E(VDW )=-225.306 E(ELEC)=-142.953 | | E(CDIH)=7.512 E(NOE )=251.049 E(PLAN)=16.331 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64851 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64762 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 64782 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 64771 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64815 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64830 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=1217.001 E(kin)=583.750 temperature=289.273 | | Etotal =633.251 grad(E)=65.926 E(BOND)=221.220 E(ANGL)=424.693 | | E(DIHE)=0.000 E(IMPR)=90.245 E(VDW )=-228.043 E(ELEC)=-152.887 | | E(CDIH)=11.118 E(NOE )=250.719 E(PLAN)=16.186 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64913 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64991 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65047 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64989 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64927 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=1204.058 E(kin)=609.049 temperature=301.809 | | Etotal =595.009 grad(E)=66.706 E(BOND)=219.511 E(ANGL)=400.243 | | E(DIHE)=0.000 E(IMPR)=94.245 E(VDW )=-224.571 E(ELEC)=-153.387 | | E(CDIH)=11.196 E(NOE )=225.559 E(PLAN)=22.214 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1214.501 E(kin)=605.512 temperature=300.057 | | Etotal =608.989 grad(E)=66.066 E(BOND)=226.172 E(ANGL)=400.794 | | E(DIHE)=0.000 E(IMPR)=90.698 E(VDW )=-230.838 E(ELEC)=-150.017 | | E(CDIH)=8.915 E(NOE )=247.208 E(PLAN)=16.058 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.696 E(kin)=12.063 temperature=5.978 | | Etotal =15.020 grad(E)=1.266 E(BOND)=10.351 E(ANGL)=12.400 | | E(DIHE)=0.000 E(IMPR)=5.928 E(VDW )=7.161 E(ELEC)=5.088 | | E(CDIH)=3.013 E(NOE )=10.186 E(PLAN)=2.067 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=1216.342 E(kin)=605.182 temperature=299.893 | | Etotal =611.160 grad(E)=65.791 E(BOND)=218.958 E(ANGL)=397.441 | | E(DIHE)=0.000 E(IMPR)=93.538 E(VDW )=-230.884 E(ELEC)=-141.949 | | E(CDIH)=8.959 E(NOE )=249.136 E(PLAN)=15.962 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=18.166 E(kin)=14.076 temperature=6.975 | | Etotal =18.473 grad(E)=1.833 E(BOND)=12.376 E(ANGL)=14.136 | | E(DIHE)=0.000 E(IMPR)=7.051 E(VDW )=8.722 E(ELEC)=8.948 | | E(CDIH)=3.059 E(NOE )=10.463 E(PLAN)=2.343 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64801 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64745 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64665 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64591 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64410 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64400 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=1212.822 E(kin)=601.254 temperature=297.946 | | Etotal =611.569 grad(E)=67.424 E(BOND)=231.476 E(ANGL)=422.420 | | E(DIHE)=0.000 E(IMPR)=91.315 E(VDW )=-240.046 E(ELEC)=-152.259 | | E(CDIH)=13.066 E(NOE )=228.679 E(PLAN)=16.917 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64397 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 64282 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64236 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64272 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64322 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64286 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 64346 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64474 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=1225.511 E(kin)=589.810 temperature=292.276 | | Etotal =635.701 grad(E)=67.598 E(BOND)=229.982 E(ANGL)=422.559 | | E(DIHE)=0.000 E(IMPR)=101.408 E(VDW )=-225.026 E(ELEC)=-149.930 | | E(CDIH)=6.050 E(NOE )=237.726 E(PLAN)=12.931 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64506 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64516 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64491 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -10 -CYT -HO2'" 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 64452 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64477 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 64451 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 64436 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 64407 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=1220.600 E(kin)=626.460 temperature=310.437 | | Etotal =594.140 grad(E)=65.716 E(BOND)=220.288 E(ANGL)=371.686 | | E(DIHE)=0.000 E(IMPR)=102.957 E(VDW )=-231.789 E(ELEC)=-147.898 | | E(CDIH)=11.100 E(NOE )=256.786 E(PLAN)=11.010 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64439 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64449 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64405 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 64443 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64477 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64553 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64564 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64629 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=1215.885 E(kin)=611.088 temperature=302.820 | | Etotal =604.797 grad(E)=64.658 E(BOND)=217.463 E(ANGL)=395.555 | | E(DIHE)=0.000 E(IMPR)=91.339 E(VDW )=-227.342 E(ELEC)=-147.858 | | E(CDIH)=12.720 E(NOE )=246.090 E(PLAN)=16.831 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64698 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 64805 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64889 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64937 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 64957 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65039 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65034 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65091 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=1202.286 E(kin)=587.230 temperature=290.997 | | Etotal =615.056 grad(E)=68.228 E(BOND)=216.482 E(ANGL)=395.240 | | E(DIHE)=0.000 E(IMPR)=101.565 E(VDW )=-234.873 E(ELEC)=-146.529 | | E(CDIH)=10.809 E(NOE )=257.184 E(PLAN)=15.178 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65091 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65141 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65195 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65209 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65211 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65191 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 65211 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=1215.258 E(kin)=596.843 temperature=295.761 | | Etotal =618.415 grad(E)=66.198 E(BOND)=218.740 E(ANGL)=416.536 | | E(DIHE)=0.000 E(IMPR)=106.182 E(VDW )=-244.330 E(ELEC)=-138.575 | | E(CDIH)=12.426 E(NOE )=233.526 E(PLAN)=13.909 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 65271 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 65371 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65357 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65390 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65402 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65425 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65462 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65503 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=1218.222 E(kin)=591.475 temperature=293.101 | | Etotal =626.747 grad(E)=66.269 E(BOND)=237.243 E(ANGL)=394.777 | | E(DIHE)=0.000 E(IMPR)=89.042 E(VDW )=-236.609 E(ELEC)=-124.296 | | E(CDIH)=7.571 E(NOE )=243.560 E(PLAN)=15.458 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65511 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65548 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65586 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65583 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65582 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65635 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=1225.152 E(kin)=608.134 temperature=301.356 | | Etotal =617.018 grad(E)=67.906 E(BOND)=213.639 E(ANGL)=410.534 | | E(DIHE)=0.000 E(IMPR)=91.908 E(VDW )=-232.994 E(ELEC)=-129.136 | | E(CDIH)=12.651 E(NOE )=234.132 E(PLAN)=16.284 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65673 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65736 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65745 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65839 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65856 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65917 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 65913 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65952 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=1229.014 E(kin)=626.731 temperature=310.571 | | Etotal =602.283 grad(E)=64.441 E(BOND)=225.903 E(ANGL)=396.748 | | E(DIHE)=0.000 E(IMPR)=95.106 E(VDW )=-238.908 E(ELEC)=-141.504 | | E(CDIH)=5.370 E(NOE )=247.101 E(PLAN)=12.467 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65899 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65904 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart NBONDS: found 65849 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65781 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65767 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65657 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=1224.844 E(kin)=605.236 temperature=299.920 | | Etotal =619.608 grad(E)=66.436 E(BOND)=234.479 E(ANGL)=403.973 | | E(DIHE)=0.000 E(IMPR)=98.734 E(VDW )=-228.351 E(ELEC)=-146.068 | | E(CDIH)=6.492 E(NOE )=234.726 E(PLAN)=15.624 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1218.763 E(kin)=605.392 temperature=299.997 | | Etotal =613.371 grad(E)=66.619 E(BOND)=226.137 E(ANGL)=397.283 | | E(DIHE)=0.000 E(IMPR)=97.147 E(VDW )=-231.072 E(ELEC)=-142.384 | | E(CDIH)=8.966 E(NOE )=241.807 E(PLAN)=15.487 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.698 E(kin)=12.282 temperature=6.086 | | Etotal =15.234 grad(E)=1.378 E(BOND)=10.655 E(ANGL)=12.404 | | E(DIHE)=0.000 E(IMPR)=6.591 E(VDW )=7.810 E(ELEC)=8.244 | | E(CDIH)=3.119 E(NOE )=9.028 E(PLAN)=2.020 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=1216.644 E(kin)=605.208 temperature=299.906 | | Etotal =611.436 grad(E)=65.895 E(BOND)=219.855 E(ANGL)=397.421 | | E(DIHE)=0.000 E(IMPR)=93.989 E(VDW )=-230.908 E(ELEC)=-142.003 | | E(CDIH)=8.959 E(NOE )=248.220 E(PLAN)=15.903 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=17.354 E(kin)=13.865 temperature=6.871 | | Etotal =18.115 grad(E)=1.803 E(BOND)=12.403 E(ANGL)=13.931 | | E(DIHE)=0.000 E(IMPR)=7.097 E(VDW )=8.614 E(ELEC)=8.864 | | E(CDIH)=3.067 E(NOE )=10.576 E(PLAN)=2.310 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65554 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65555 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65488 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65477 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65522 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 65611 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65726 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=1210.267 E(kin)=602.814 temperature=298.720 | | Etotal =607.453 grad(E)=66.849 E(BOND)=240.314 E(ANGL)=375.925 | | E(DIHE)=0.000 E(IMPR)=90.866 E(VDW )=-230.919 E(ELEC)=-149.996 | | E(CDIH)=10.315 E(NOE )=251.702 E(PLAN)=19.246 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65744 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65823 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65883 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65895 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65864 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65799 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=1221.414 E(kin)=589.404 temperature=292.074 | | Etotal =632.010 grad(E)=69.313 E(BOND)=222.115 E(ANGL)=406.864 | | E(DIHE)=0.000 E(IMPR)=116.125 E(VDW )=-240.444 E(ELEC)=-144.019 | | E(CDIH)=4.277 E(NOE )=251.194 E(PLAN)=15.898 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65787 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65787 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65862 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65837 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65854 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=1221.101 E(kin)=600.552 temperature=297.599 | | Etotal =620.549 grad(E)=67.832 E(BOND)=234.482 E(ANGL)=396.810 | | E(DIHE)=0.000 E(IMPR)=100.786 E(VDW )=-238.732 E(ELEC)=-152.898 | | E(CDIH)=8.598 E(NOE )=253.282 E(PLAN)=18.222 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65899 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65862 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65900 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65994 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66053 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66224 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66201 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=1221.938 E(kin)=604.948 temperature=299.777 | | Etotal =616.990 grad(E)=66.753 E(BOND)=228.661 E(ANGL)=394.429 | | E(DIHE)=0.000 E(IMPR)=105.383 E(VDW )=-242.023 E(ELEC)=-142.198 | | E(CDIH)=7.600 E(NOE )=245.481 E(PLAN)=19.657 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66212 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66185 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66183 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66212 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66280 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66317 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=1225.991 E(kin)=612.860 temperature=303.698 | | Etotal =613.131 grad(E)=68.018 E(BOND)=215.532 E(ANGL)=401.951 | | E(DIHE)=0.000 E(IMPR)=98.439 E(VDW )=-230.662 E(ELEC)=-147.767 | | E(CDIH)=7.059 E(NOE )=251.855 E(PLAN)=16.724 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66350 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66323 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66362 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66387 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 66367 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66373 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.43 A apart NBONDS: found 66361 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=1206.371 E(kin)=602.536 temperature=298.582 | | Etotal =603.835 grad(E)=64.453 E(BOND)=217.949 E(ANGL)=398.915 | | E(DIHE)=0.000 E(IMPR)=104.788 E(VDW )=-245.826 E(ELEC)=-148.613 | | E(CDIH)=10.548 E(NOE )=253.226 E(PLAN)=12.849 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart NBONDS: found 66368 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66274 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 66180 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -10 -CYT -HO2'" 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 66057 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65964 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65883 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65863 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=1209.378 E(kin)=583.888 temperature=289.341 | | Etotal =625.490 grad(E)=69.496 E(BOND)=228.505 E(ANGL)=395.630 | | E(DIHE)=0.000 E(IMPR)=106.086 E(VDW )=-239.869 E(ELEC)=-140.964 | | E(CDIH)=12.154 E(NOE )=249.400 E(PLAN)=14.548 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65892 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65948 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65986 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66190 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66290 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -10 -CYT -HO2'" 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 66373 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66430 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66539 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=1208.317 E(kin)=600.840 temperature=297.741 | | Etotal =607.477 grad(E)=66.084 E(BOND)=230.156 E(ANGL)=386.921 | | E(DIHE)=0.000 E(IMPR)=100.689 E(VDW )=-238.712 E(ELEC)=-142.390 | | E(CDIH)=7.493 E(NOE )=249.378 E(PLAN)=13.940 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66495 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66458 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66384 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66366 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 66261 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66230 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66213 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66089 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=1230.627 E(kin)=615.132 temperature=304.824 | | Etotal =615.495 grad(E)=67.224 E(BOND)=229.375 E(ANGL)=402.950 | | E(DIHE)=0.000 E(IMPR)=87.169 E(VDW )=-245.750 E(ELEC)=-140.212 | | E(CDIH)=7.610 E(NOE )=255.908 E(PLAN)=18.446 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66008 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 65952 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65883 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65887 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65751 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65855 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65837 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65877 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=1214.875 E(kin)=602.563 temperature=298.595 | | Etotal =612.312 grad(E)=67.158 E(BOND)=246.893 E(ANGL)=385.496 | | E(DIHE)=0.000 E(IMPR)=88.573 E(VDW )=-241.411 E(ELEC)=-128.126 | | E(CDIH)=8.056 E(NOE )=239.224 E(PLAN)=13.607 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1218.098 E(kin)=605.514 temperature=300.058 | | Etotal =612.584 grad(E)=67.335 E(BOND)=226.140 E(ANGL)=398.687 | | E(DIHE)=0.000 E(IMPR)=97.783 E(VDW )=-238.372 E(ELEC)=-143.473 | | E(CDIH)=7.652 E(NOE )=248.250 E(PLAN)=15.917 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.536 E(kin)=12.121 temperature=6.006 | | Etotal =14.953 grad(E)=1.289 E(BOND)=10.227 E(ANGL)=12.650 | | E(DIHE)=0.000 E(IMPR)=7.468 E(VDW )=6.985 E(ELEC)=6.272 | | E(CDIH)=2.722 E(NOE )=9.005 E(PLAN)=2.226 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=1216.806 E(kin)=605.242 temperature=299.923 | | Etotal =611.563 grad(E)=66.055 E(BOND)=220.553 E(ANGL)=397.562 | | E(DIHE)=0.000 E(IMPR)=94.410 E(VDW )=-231.737 E(ELEC)=-142.167 | | E(CDIH)=8.814 E(NOE )=248.223 E(PLAN)=15.904 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=16.673 E(kin)=13.682 temperature=6.780 | | Etotal =17.795 grad(E)=1.811 E(BOND)=12.340 E(ANGL)=13.801 | | E(DIHE)=0.000 E(IMPR)=7.238 E(VDW )=8.768 E(ELEC)=8.627 | | E(CDIH)=3.058 E(NOE )=10.413 E(PLAN)=2.301 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65979 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66039 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66132 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66078 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66074 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66055 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65943 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65846 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65740 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=1202.548 E(kin)=592.105 temperature=293.413 | | Etotal =610.444 grad(E)=68.235 E(BOND)=231.417 E(ANGL)=374.353 | | E(DIHE)=0.000 E(IMPR)=102.334 E(VDW )=-223.421 E(ELEC)=-146.443 | | E(CDIH)=7.763 E(NOE )=254.464 E(PLAN)=9.976 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65681 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65631 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65500 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65498 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 65485 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65509 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65492 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 65512 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65522 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65557 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=1219.635 E(kin)=608.179 temperature=301.378 | | Etotal =611.457 grad(E)=67.481 E(BOND)=219.961 E(ANGL)=413.346 | | E(DIHE)=0.000 E(IMPR)=101.327 E(VDW )=-241.495 E(ELEC)=-145.867 | | E(CDIH)=8.846 E(NOE )=241.484 E(PLAN)=13.855 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 65566 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65598 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65648 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65743 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65925 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66029 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66128 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66190 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -10 -CYT -HO2'" 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 66251 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66280 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=1209.140 E(kin)=584.069 temperature=289.431 | | Etotal =625.071 grad(E)=70.001 E(BOND)=211.152 E(ANGL)=414.293 | | E(DIHE)=0.000 E(IMPR)=93.773 E(VDW )=-234.711 E(ELEC)=-144.269 | | E(CDIH)=13.483 E(NOE )=253.260 E(PLAN)=18.090 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66277 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66340 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66412 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66407 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66391 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66381 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66345 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66321 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 66378 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=1220.396 E(kin)=612.414 temperature=303.477 | | Etotal =607.982 grad(E)=66.965 E(BOND)=228.722 E(ANGL)=393.410 | | E(DIHE)=0.000 E(IMPR)=90.768 E(VDW )=-230.890 E(ELEC)=-143.070 | | E(CDIH)=10.815 E(NOE )=241.463 E(PLAN)=16.762 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66388 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66420 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66428 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66458 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66500 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66558 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 66557 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66589 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 66613 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=1229.455 E(kin)=623.938 temperature=309.187 | | Etotal =605.517 grad(E)=66.342 E(BOND)=205.490 E(ANGL)=408.795 | | E(DIHE)=0.000 E(IMPR)=104.137 E(VDW )=-244.868 E(ELEC)=-132.816 | | E(CDIH)=3.314 E(NOE )=249.558 E(PLAN)=11.907 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66620 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66652 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66628 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66579 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66626 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 66630 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66673 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66715 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66752 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66767 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=1222.637 E(kin)=635.874 temperature=315.102 | | Etotal =586.763 grad(E)=65.994 E(BOND)=216.614 E(ANGL)=398.828 | | E(DIHE)=0.000 E(IMPR)=83.794 E(VDW )=-227.072 E(ELEC)=-147.446 | | E(CDIH)=6.155 E(NOE )=243.176 E(PLAN)=12.712 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66774 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66714 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66723 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66723 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66707 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66677 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66654 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66642 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66595 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66609 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66610 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=1201.692 E(kin)=600.704 temperature=297.674 | | Etotal =600.989 grad(E)=67.709 E(BOND)=234.036 E(ANGL)=380.533 | | E(DIHE)=0.000 E(IMPR)=96.467 E(VDW )=-234.794 E(ELEC)=-148.202 | | E(CDIH)=12.475 E(NOE )=245.285 E(PLAN)=15.190 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66619 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66688 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 66637 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66602 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66559 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66522 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66555 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66589 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66608 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66609 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=1221.197 E(kin)=595.718 temperature=295.203 | | Etotal =625.479 grad(E)=68.704 E(BOND)=216.385 E(ANGL)=412.074 | | E(DIHE)=0.000 E(IMPR)=97.626 E(VDW )=-233.237 E(ELEC)=-140.117 | | E(CDIH)=4.218 E(NOE )=255.766 E(PLAN)=12.765 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66624 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66764 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66805 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66794 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66790 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66780 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=1218.239 E(kin)=603.131 temperature=298.877 | | Etotal =615.108 grad(E)=69.729 E(BOND)=223.084 E(ANGL)=397.242 | | E(DIHE)=0.000 E(IMPR)=98.794 E(VDW )=-238.758 E(ELEC)=-140.437 | | E(CDIH)=10.454 E(NOE )=248.701 E(PLAN)=16.029 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 66700 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66641 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66580 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66469 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66426 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66427 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66517 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=1230.488 E(kin)=581.320 temperature=288.069 | | Etotal =649.167 grad(E)=68.946 E(BOND)=234.224 E(ANGL)=418.066 | | E(DIHE)=0.000 E(IMPR)=106.179 E(VDW )=-241.500 E(ELEC)=-146.655 | | E(CDIH)=14.722 E(NOE )=243.858 E(PLAN)=20.275 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1220.505 E(kin)=605.408 temperature=300.005 | | Etotal =615.097 grad(E)=67.636 E(BOND)=226.532 E(ANGL)=400.427 | | E(DIHE)=0.000 E(IMPR)=95.662 E(VDW )=-235.113 E(ELEC)=-143.864 | | E(CDIH)=8.326 E(NOE )=247.935 E(PLAN)=15.193 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.405 E(kin)=12.170 temperature=6.031 | | Etotal =14.927 grad(E)=1.299 E(BOND)=10.792 E(ANGL)=12.195 | | E(DIHE)=0.000 E(IMPR)=6.476 E(VDW )=7.895 E(ELEC)=6.659 | | E(CDIH)=2.856 E(NOE )=9.052 E(PLAN)=2.167 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=1217.176 E(kin)=605.259 temperature=299.931 | | Etotal =611.917 grad(E)=66.213 E(BOND)=221.151 E(ANGL)=397.849 | | E(DIHE)=0.000 E(IMPR)=94.535 E(VDW )=-232.075 E(ELEC)=-142.336 | | E(CDIH)=8.765 E(NOE )=248.194 E(PLAN)=15.833 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=16.133 E(kin)=13.539 temperature=6.709 | | Etotal =17.561 grad(E)=1.829 E(BOND)=12.325 E(ANGL)=13.676 | | E(DIHE)=0.000 E(IMPR)=7.175 E(VDW )=8.743 E(ELEC)=8.466 | | E(CDIH)=3.042 E(NOE )=10.286 E(PLAN)=2.298 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66505 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66622 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66691 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66750 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66796 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66779 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=1216.773 E(kin)=614.155 temperature=304.340 | | Etotal =602.618 grad(E)=68.084 E(BOND)=215.061 E(ANGL)=403.663 | | E(DIHE)=0.000 E(IMPR)=85.687 E(VDW )=-227.264 E(ELEC)=-147.136 | | E(CDIH)=6.756 E(NOE )=250.757 E(PLAN)=15.094 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66777 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66734 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66770 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66787 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66842 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66868 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=1205.614 E(kin)=618.879 temperature=306.681 | | Etotal =586.735 grad(E)=66.262 E(BOND)=212.823 E(ANGL)=391.013 | | E(DIHE)=0.000 E(IMPR)=95.181 E(VDW )=-230.397 E(ELEC)=-150.722 | | E(CDIH)=11.576 E(NOE )=242.424 E(PLAN)=14.836 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66911 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66968 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 67020 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66978 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66974 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=1198.066 E(kin)=577.772 temperature=286.310 | | Etotal =620.294 grad(E)=68.863 E(BOND)=220.339 E(ANGL)=426.106 | | E(DIHE)=0.000 E(IMPR)=91.985 E(VDW )=-244.857 E(ELEC)=-148.269 | | E(CDIH)=6.660 E(NOE )=254.307 E(PLAN)=14.022 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 67053 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart NBONDS: found 67021 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 66953 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 67043 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 67005 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=1229.230 E(kin)=611.076 temperature=302.814 | | Etotal =618.154 grad(E)=68.151 E(BOND)=239.950 E(ANGL)=402.855 | | E(DIHE)=0.000 E(IMPR)=102.328 E(VDW )=-239.003 E(ELEC)=-148.008 | | E(CDIH)=8.789 E(NOE )=235.997 E(PLAN)=15.245 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67023 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67049 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 67026 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 67148 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 67188 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 67282 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 67356 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 67478 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=1206.099 E(kin)=612.071 temperature=303.307 | | Etotal =594.028 grad(E)=69.362 E(BOND)=232.267 E(ANGL)=393.298 | | E(DIHE)=0.000 E(IMPR)=97.786 E(VDW )=-238.906 E(ELEC)=-145.217 | | E(CDIH)=7.311 E(NOE )=231.152 E(PLAN)=16.337 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 67534 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 67569 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 67575 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 67533 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67431 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=1221.474 E(kin)=614.335 temperature=304.429 | | Etotal =607.139 grad(E)=67.902 E(BOND)=235.488 E(ANGL)=375.756 | | E(DIHE)=0.000 E(IMPR)=104.325 E(VDW )=-246.651 E(ELEC)=-151.807 | | E(CDIH)=7.598 E(NOE )=266.095 E(PLAN)=16.336 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 67336 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 67243 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 67120 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 67077 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 67005 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66985 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=1218.730 E(kin)=599.081 temperature=296.870 | | Etotal =619.649 grad(E)=68.861 E(BOND)=214.873 E(ANGL)=408.501 | | E(DIHE)=0.000 E(IMPR)=116.345 E(VDW )=-251.216 E(ELEC)=-143.993 | | E(CDIH)=7.040 E(NOE )=257.134 E(PLAN)=10.966 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 67001 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66939 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66931 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66925 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66892 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66833 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66788 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=1228.730 E(kin)=635.200 temperature=314.768 | | Etotal =593.530 grad(E)=66.290 E(BOND)=209.301 E(ANGL)=400.035 | | E(DIHE)=0.000 E(IMPR)=101.948 E(VDW )=-243.398 E(ELEC)=-151.448 | | E(CDIH)=5.808 E(NOE )=253.332 E(PLAN)=17.953 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart NBONDS: found 66796 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 66811 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66833 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 66907 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66995 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=1213.333 E(kin)=602.482 temperature=298.555 | | Etotal =610.851 grad(E)=68.308 E(BOND)=221.283 E(ANGL)=411.482 | | E(DIHE)=0.000 E(IMPR)=101.160 E(VDW )=-248.911 E(ELEC)=-144.142 | | E(CDIH)=12.148 E(NOE )=242.217 E(PLAN)=15.614 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66930 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66998 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 67084 intra-atom interactions %atoms "A -8 -CYT -HO2'" and "A -9 -URI -H5' " only 1.45 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67105 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67008 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66975 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=1226.873 E(kin)=610.719 temperature=302.637 | | Etotal =616.154 grad(E)=66.184 E(BOND)=217.408 E(ANGL)=403.245 | | E(DIHE)=0.000 E(IMPR)=96.077 E(VDW )=-234.142 E(ELEC)=-142.335 | | E(CDIH)=12.038 E(NOE )=245.529 E(PLAN)=18.335 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1218.493 E(kin)=605.521 temperature=300.061 | | Etotal =612.972 grad(E)=67.752 E(BOND)=226.766 E(ANGL)=404.050 | | E(DIHE)=0.000 E(IMPR)=97.924 E(VDW )=-239.946 E(ELEC)=-147.999 | | E(CDIH)=8.048 E(NOE )=248.319 E(PLAN)=15.811 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.876 E(kin)=12.783 temperature=6.335 | | Etotal =15.117 grad(E)=1.385 E(BOND)=10.703 E(ANGL)=12.652 | | E(DIHE)=0.000 E(IMPR)=6.889 E(VDW )=7.064 E(ELEC)=3.455 | | E(CDIH)=2.485 E(NOE )=9.189 E(PLAN)=2.086 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=1217.295 E(kin)=605.283 temperature=299.943 | | Etotal =612.013 grad(E)=66.353 E(BOND)=221.662 E(ANGL)=398.412 | | E(DIHE)=0.000 E(IMPR)=94.843 E(VDW )=-232.790 E(ELEC)=-142.851 | | E(CDIH)=8.700 E(NOE )=248.206 E(PLAN)=15.831 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=15.618 E(kin)=13.472 temperature=6.676 | | Etotal =17.356 grad(E)=1.847 E(BOND)=12.293 E(ANGL)=13.702 | | E(DIHE)=0.000 E(IMPR)=7.216 E(VDW )=8.897 E(ELEC)=8.300 | | E(CDIH)=3.003 E(NOE )=10.191 E(PLAN)=2.279 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66944 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66841 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66771 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66684 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66677 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66668 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66633 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66565 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=1220.921 E(kin)=590.855 temperature=292.793 | | Etotal =630.067 grad(E)=67.890 E(BOND)=220.355 E(ANGL)=434.114 | | E(DIHE)=0.000 E(IMPR)=92.427 E(VDW )=-245.612 E(ELEC)=-145.183 | | E(CDIH)=12.824 E(NOE )=246.976 E(PLAN)=14.166 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66537 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66451 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66479 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66490 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66540 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66565 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 66572 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=1222.097 E(kin)=593.751 temperature=294.228 | | Etotal =628.347 grad(E)=67.881 E(BOND)=240.114 E(ANGL)=415.154 | | E(DIHE)=0.000 E(IMPR)=96.352 E(VDW )=-234.883 E(ELEC)=-150.446 | | E(CDIH)=11.202 E(NOE )=237.357 E(PLAN)=13.497 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66572 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66569 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart NBONDS: found 66535 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66603 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66667 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66729 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66807 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=1235.012 E(kin)=621.075 temperature=307.769 | | Etotal =613.937 grad(E)=68.010 E(BOND)=231.223 E(ANGL)=414.967 | | E(DIHE)=0.000 E(IMPR)=87.629 E(VDW )=-237.912 E(ELEC)=-146.923 | | E(CDIH)=8.073 E(NOE )=241.624 E(PLAN)=15.256 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66809 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66866 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 66866 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66866 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66797 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66749 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66745 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66777 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=1214.637 E(kin)=615.065 temperature=304.791 | | Etotal =599.571 grad(E)=65.887 E(BOND)=209.558 E(ANGL)=408.007 | | E(DIHE)=0.000 E(IMPR)=85.062 E(VDW )=-221.865 E(ELEC)=-147.442 | | E(CDIH)=9.071 E(NOE )=239.181 E(PLAN)=18.000 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66700 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66680 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66647 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 66616 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66542 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart NBONDS: found 66495 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart NBONDS: found 66477 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=1216.234 E(kin)=603.624 temperature=299.121 | | Etotal =612.610 grad(E)=66.661 E(BOND)=224.393 E(ANGL)=406.021 | | E(DIHE)=0.000 E(IMPR)=89.964 E(VDW )=-244.090 E(ELEC)=-143.837 | | E(CDIH)=8.413 E(NOE )=257.697 E(PLAN)=14.049 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66488 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66554 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66570 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.36 A apart NBONDS: found 66577 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66571 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66565 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66472 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.18 A apart NBONDS: found 66537 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=1229.841 E(kin)=591.219 temperature=292.974 | | Etotal =638.622 grad(E)=70.016 E(BOND)=245.690 E(ANGL)=402.761 | | E(DIHE)=0.000 E(IMPR)=111.418 E(VDW )=-229.608 E(ELEC)=-145.521 | | E(CDIH)=3.583 E(NOE )=236.659 E(PLAN)=13.640 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66547 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66524 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66539 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66575 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 66557 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66586 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66571 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66563 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66563 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=1222.362 E(kin)=590.867 temperature=292.800 | | Etotal =631.494 grad(E)=67.658 E(BOND)=228.534 E(ANGL)=401.139 | | E(DIHE)=0.000 E(IMPR)=95.778 E(VDW )=-236.289 E(ELEC)=-143.422 | | E(CDIH)=9.854 E(NOE )=258.768 E(PLAN)=17.132 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66642 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66652 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66647 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66694 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66751 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66795 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66861 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66936 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66942 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=1222.585 E(kin)=599.679 temperature=297.166 | | Etotal =622.906 grad(E)=69.141 E(BOND)=235.310 E(ANGL)=406.279 | | E(DIHE)=0.000 E(IMPR)=94.939 E(VDW )=-231.368 E(ELEC)=-144.856 | | E(CDIH)=6.110 E(NOE )=240.743 E(PLAN)=15.750 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66931 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66905 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66922 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66889 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66872 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66880 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 66901 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66885 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.45 A apart NBONDS: found 66870 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=1214.964 E(kin)=602.227 temperature=298.429 | | Etotal =612.737 grad(E)=68.186 E(BOND)=234.652 E(ANGL)=395.511 | | E(DIHE)=0.000 E(IMPR)=89.449 E(VDW )=-244.607 E(ELEC)=-132.475 | | E(CDIH)=10.712 E(NOE )=245.827 E(PLAN)=13.668 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 66914 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66960 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66968 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 66901 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66899 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -10 -CYT -HO2'" and "A -13 -ADE -H62 " only 1.44 A apart NBONDS: found 66775 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66699 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66669 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66621 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=1220.829 E(kin)=605.834 temperature=300.216 | | Etotal =614.995 grad(E)=67.556 E(BOND)=216.909 E(ANGL)=418.372 | | E(DIHE)=0.000 E(IMPR)=99.169 E(VDW )=-247.199 E(ELEC)=-146.159 | | E(CDIH)=17.405 E(NOE )=239.940 E(PLAN)=16.558 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1219.623 E(kin)=605.500 temperature=300.051 | | Etotal =614.122 grad(E)=67.613 E(BOND)=224.555 E(ANGL)=405.192 | | E(DIHE)=0.000 E(IMPR)=95.930 E(VDW )=-238.922 E(ELEC)=-144.581 | | E(CDIH)=8.159 E(NOE )=248.338 E(PLAN)=15.452 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.048 E(kin)=12.567 temperature=6.228 | | Etotal =15.032 grad(E)=1.417 E(BOND)=10.502 E(ANGL)=12.353 | | E(DIHE)=0.000 E(IMPR)=6.477 E(VDW )=8.118 E(ELEC)=4.202 | | E(CDIH)=2.925 E(NOE )=9.313 E(PLAN)=1.861 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=1217.489 E(kin)=605.301 temperature=299.952 | | Etotal =612.189 grad(E)=66.458 E(BOND)=221.903 E(ANGL)=398.977 | | E(DIHE)=0.000 E(IMPR)=94.934 E(VDW )=-233.301 E(ELEC)=-142.995 | | E(CDIH)=8.655 E(NOE )=248.217 E(PLAN)=15.800 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=15.193 E(kin)=13.399 temperature=6.640 | | Etotal =17.184 grad(E)=1.848 E(BOND)=12.180 E(ANGL)=13.723 | | E(DIHE)=0.000 E(IMPR)=7.163 E(VDW )=8.996 E(ELEC)=8.053 | | E(CDIH)=3.000 E(NOE )=10.121 E(PLAN)=2.250 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66620 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66650 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 66647 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 66666 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 66772 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66856 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66964 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 67094 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 67183 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=1224.077 E(kin)=607.084 temperature=300.835 | | Etotal =616.994 grad(E)=68.204 E(BOND)=220.217 E(ANGL)=401.960 | | E(DIHE)=0.000 E(IMPR)=97.890 E(VDW )=-223.499 E(ELEC)=-149.444 | | E(CDIH)=6.437 E(NOE )=245.803 E(PLAN)=17.631 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 67213 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67282 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67243 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 67163 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67100 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67101 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 67011 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66947 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=1214.353 E(kin)=599.321 temperature=296.989 | | Etotal =615.032 grad(E)=69.765 E(BOND)=223.274 E(ANGL)=414.731 | | E(DIHE)=0.000 E(IMPR)=92.336 E(VDW )=-238.807 E(ELEC)=-137.733 | | E(CDIH)=12.623 E(NOE )=235.229 E(PLAN)=13.378 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 66846 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart NBONDS: found 66752 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66730 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66676 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66753 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66845 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66936 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=1228.582 E(kin)=581.005 temperature=287.912 | | Etotal =647.577 grad(E)=69.191 E(BOND)=240.343 E(ANGL)=428.304 | | E(DIHE)=0.000 E(IMPR)=105.550 E(VDW )=-242.522 E(ELEC)=-140.193 | | E(CDIH)=8.948 E(NOE )=235.264 E(PLAN)=11.885 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 67202 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67202 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 67191 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67234 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 67321 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 67392 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 67448 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=1206.338 E(kin)=595.610 temperature=295.150 | | Etotal =610.728 grad(E)=69.762 E(BOND)=222.461 E(ANGL)=399.460 | | E(DIHE)=0.000 E(IMPR)=101.806 E(VDW )=-241.696 E(ELEC)=-144.638 | | E(CDIH)=10.676 E(NOE )=248.050 E(PLAN)=14.610 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 67454 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 67374 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 67357 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.45 A apart NBONDS: found 67259 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 67295 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 67315 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67340 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=1202.841 E(kin)=616.690 temperature=305.596 | | Etotal =586.151 grad(E)=67.139 E(BOND)=211.165 E(ANGL)=397.218 | | E(DIHE)=0.000 E(IMPR)=99.043 E(VDW )=-240.713 E(ELEC)=-143.984 | | E(CDIH)=11.139 E(NOE )=237.577 E(PLAN)=14.704 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 67389 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 67393 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 67364 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 67456 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 67554 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67517 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.44 A apart NBONDS: found 67478 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67520 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67399 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=1214.746 E(kin)=613.139 temperature=303.836 | | Etotal =601.607 grad(E)=66.883 E(BOND)=245.281 E(ANGL)=394.565 | | E(DIHE)=0.000 E(IMPR)=92.268 E(VDW )=-240.915 E(ELEC)=-155.753 | | E(CDIH)=11.506 E(NOE )=237.290 E(PLAN)=17.364 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 67379 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 67396 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67282 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 67227 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67079 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 67069 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 67025 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=1215.513 E(kin)=588.114 temperature=291.435 | | Etotal =627.399 grad(E)=69.953 E(BOND)=224.169 E(ANGL)=424.415 | | E(DIHE)=0.000 E(IMPR)=99.695 E(VDW )=-258.525 E(ELEC)=-142.238 | | E(CDIH)=7.816 E(NOE )=258.869 E(PLAN)=13.198 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 67029 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67074 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67105 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 67176 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67183 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 67171 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 67163 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 67231 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 67282 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=1212.274 E(kin)=598.606 temperature=296.634 | | Etotal =613.668 grad(E)=67.284 E(BOND)=235.601 E(ANGL)=397.609 | | E(DIHE)=0.000 E(IMPR)=88.259 E(VDW )=-245.976 E(ELEC)=-146.900 | | E(CDIH)=5.956 E(NOE )=262.038 E(PLAN)=17.082 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67312 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 67314 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 67361 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 67367 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 67400 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 67423 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67343 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.41 A apart NBONDS: found 67197 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=1215.143 E(kin)=615.033 temperature=304.775 | | Etotal =600.110 grad(E)=67.769 E(BOND)=237.594 E(ANGL)=389.546 | | E(DIHE)=0.000 E(IMPR)=89.270 E(VDW )=-238.871 E(ELEC)=-155.083 | | E(CDIH)=9.345 E(NOE )=249.750 E(PLAN)=18.558 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 67195 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 67122 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 67054 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 67050 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 66994 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.17 A apart NBONDS: found 66963 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 66944 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 67010 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66996 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.43 A apart NBONDS: found 67019 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.49 A apart NBONDS: found 67028 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=1229.332 E(kin)=604.005 temperature=299.310 | | Etotal =625.327 grad(E)=70.449 E(BOND)=226.547 E(ANGL)=409.526 | | E(DIHE)=0.000 E(IMPR)=106.305 E(VDW )=-226.283 E(ELEC)=-150.029 | | E(CDIH)=12.663 E(NOE )=228.369 E(PLAN)=18.228 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1217.875 E(kin)=605.454 temperature=300.028 | | Etotal =612.421 grad(E)=68.849 E(BOND)=227.281 E(ANGL)=405.846 | | E(DIHE)=0.000 E(IMPR)=96.812 E(VDW )=-240.982 E(ELEC)=-147.611 | | E(CDIH)=8.383 E(NOE )=247.741 E(PLAN)=14.949 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.256 E(kin)=12.145 temperature=6.018 | | Etotal =14.311 grad(E)=1.390 E(BOND)=9.911 E(ANGL)=13.136 | | E(DIHE)=0.000 E(IMPR)=6.155 E(VDW )=7.815 E(ELEC)=6.010 | | E(CDIH)=2.793 E(NOE )=9.362 E(PLAN)=1.804 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=1217.519 E(kin)=605.313 temperature=299.958 | | Etotal =612.206 grad(E)=66.642 E(BOND)=222.316 E(ANGL)=399.506 | | E(DIHE)=0.000 E(IMPR)=95.078 E(VDW )=-233.892 E(ELEC)=-143.350 | | E(CDIH)=8.634 E(NOE )=248.180 E(PLAN)=15.734 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=14.776 E(kin)=13.307 temperature=6.594 | | Etotal =16.981 grad(E)=1.926 E(BOND)=12.106 E(ANGL)=13.801 | | E(DIHE)=0.000 E(IMPR)=7.108 E(VDW )=9.142 E(ELEC)=8.010 | | E(CDIH)=2.986 E(NOE )=10.065 E(PLAN)=2.230 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 67055 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 67061 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 67002 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66887 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66814 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66858 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 66795 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66766 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66750 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=1224.733 E(kin)=612.262 temperature=303.402 | | Etotal =612.471 grad(E)=69.892 E(BOND)=223.158 E(ANGL)=419.892 | | E(DIHE)=0.000 E(IMPR)=91.037 E(VDW )=-240.634 E(ELEC)=-139.900 | | E(CDIH)=6.604 E(NOE )=238.111 E(PLAN)=14.202 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66710 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66654 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66673 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66572 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66575 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66569 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66587 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66628 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=1214.181 E(kin)=615.487 temperature=305.000 | | Etotal =598.694 grad(E)=68.130 E(BOND)=210.916 E(ANGL)=422.616 | | E(DIHE)=0.000 E(IMPR)=80.090 E(VDW )=-242.864 E(ELEC)=-138.973 | | E(CDIH)=9.559 E(NOE )=242.007 E(PLAN)=15.344 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66680 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66710 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66834 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66871 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66873 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66867 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66893 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=1214.370 E(kin)=593.319 temperature=294.015 | | Etotal =621.051 grad(E)=68.279 E(BOND)=218.962 E(ANGL)=409.839 | | E(DIHE)=0.000 E(IMPR)=100.135 E(VDW )=-243.265 E(ELEC)=-149.002 | | E(CDIH)=8.058 E(NOE )=257.377 E(PLAN)=18.947 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66877 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.48 A apart NBONDS: found 66820 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66759 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66681 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66570 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66529 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66419 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66433 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=1233.564 E(kin)=619.029 temperature=306.755 | | Etotal =614.536 grad(E)=66.762 E(BOND)=229.388 E(ANGL)=386.276 | | E(DIHE)=0.000 E(IMPR)=97.594 E(VDW )=-241.989 E(ELEC)=-134.690 | | E(CDIH)=8.196 E(NOE )=251.466 E(PLAN)=18.294 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66405 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66443 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66461 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66442 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66383 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 66334 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66315 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=1209.083 E(kin)=600.391 temperature=297.519 | | Etotal =608.691 grad(E)=67.461 E(BOND)=223.606 E(ANGL)=411.201 | | E(DIHE)=0.000 E(IMPR)=93.809 E(VDW )=-244.348 E(ELEC)=-142.719 | | E(CDIH)=5.202 E(NOE )=241.454 E(PLAN)=20.487 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66270 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66249 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.50 A apart NBONDS: found 66215 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66163 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66233 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66255 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66260 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66299 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=1217.747 E(kin)=599.511 temperature=297.083 | | Etotal =618.236 grad(E)=66.896 E(BOND)=215.620 E(ANGL)=408.273 | | E(DIHE)=0.000 E(IMPR)=92.968 E(VDW )=-243.744 E(ELEC)=-135.465 | | E(CDIH)=5.910 E(NOE )=256.754 E(PLAN)=17.921 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66298 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66468 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66570 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66619 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 66655 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 66642 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66677 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 66686 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66665 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=1207.554 E(kin)=611.790 temperature=303.167 | | Etotal =595.765 grad(E)=66.652 E(BOND)=233.683 E(ANGL)=387.914 | | E(DIHE)=0.000 E(IMPR)=92.213 E(VDW )=-240.737 E(ELEC)=-145.817 | | E(CDIH)=6.993 E(NOE )=246.380 E(PLAN)=15.135 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66633 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66647 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart NBONDS: found 66669 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66713 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart NBONDS: found 66745 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart NBONDS: found 66718 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66705 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=1214.067 E(kin)=598.942 temperature=296.801 | | Etotal =615.124 grad(E)=69.531 E(BOND)=231.177 E(ANGL)=402.948 | | E(DIHE)=0.000 E(IMPR)=103.618 E(VDW )=-247.420 E(ELEC)=-145.912 | | E(CDIH)=7.641 E(NOE )=246.862 E(PLAN)=16.211 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66724 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.47 A apart NBONDS: found 66700 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66737 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66737 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66778 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66748 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66758 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66683 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=1211.553 E(kin)=596.380 temperature=295.531 | | Etotal =615.173 grad(E)=67.410 E(BOND)=230.237 E(ANGL)=386.894 | | E(DIHE)=0.000 E(IMPR)=94.019 E(VDW )=-227.865 E(ELEC)=-139.024 | | E(CDIH)=7.875 E(NOE )=245.743 E(PLAN)=17.293 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66648 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66527 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66515 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66466 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66414 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66360 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66312 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66323 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=1220.006 E(kin)=592.615 temperature=293.666 | | Etotal =627.391 grad(E)=69.337 E(BOND)=230.838 E(ANGL)=417.700 | | E(DIHE)=0.000 E(IMPR)=102.265 E(VDW )=-239.740 E(ELEC)=-143.383 | | E(CDIH)=7.525 E(NOE )=238.731 E(PLAN)=13.456 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1218.778 E(kin)=605.502 temperature=300.052 | | Etotal =613.276 grad(E)=68.264 E(BOND)=225.536 E(ANGL)=403.338 | | E(DIHE)=0.000 E(IMPR)=97.234 E(VDW )=-239.761 E(ELEC)=-142.932 | | E(CDIH)=7.793 E(NOE )=246.317 E(PLAN)=15.751 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.892 E(kin)=12.385 temperature=6.137 | | Etotal =14.215 grad(E)=1.393 E(BOND)=10.565 E(ANGL)=12.375 | | E(DIHE)=0.000 E(IMPR)=6.101 E(VDW )=6.574 E(ELEC)=4.117 | | E(CDIH)=2.566 E(NOE )=8.356 E(PLAN)=2.224 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=1217.609 E(kin)=605.326 temperature=299.965 | | Etotal =612.283 grad(E)=66.758 E(BOND)=222.546 E(ANGL)=399.779 | | E(DIHE)=0.000 E(IMPR)=95.232 E(VDW )=-234.311 E(ELEC)=-143.320 | | E(CDIH)=8.574 E(NOE )=248.047 E(PLAN)=15.735 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=14.398 E(kin)=13.243 temperature=6.563 | | Etotal =16.800 grad(E)=1.938 E(BOND)=12.031 E(ANGL)=13.740 | | E(DIHE)=0.000 E(IMPR)=7.063 E(VDW )=9.109 E(ELEC)=7.797 | | E(CDIH)=2.966 E(NOE )=9.964 E(PLAN)=2.230 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66327 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66369 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart NBONDS: found 66375 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66341 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66364 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66348 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=1220.099 E(kin)=612.729 temperature=303.633 | | Etotal =607.370 grad(E)=68.705 E(BOND)=230.925 E(ANGL)=400.088 | | E(DIHE)=0.000 E(IMPR)=100.043 E(VDW )=-240.933 E(ELEC)=-146.124 | | E(CDIH)=8.332 E(NOE )=238.611 E(PLAN)=16.428 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66382 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66422 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66429 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66436 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66483 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66519 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66529 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=1212.406 E(kin)=583.260 temperature=289.030 | | Etotal =629.146 grad(E)=69.899 E(BOND)=252.326 E(ANGL)=389.687 | | E(DIHE)=0.000 E(IMPR)=95.929 E(VDW )=-228.280 E(ELEC)=-151.469 | | E(CDIH)=5.327 E(NOE )=247.171 E(PLAN)=18.454 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66537 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 66584 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66547 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 66524 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 66454 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66343 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66171 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=1223.241 E(kin)=601.412 temperature=298.025 | | Etotal =621.829 grad(E)=69.997 E(BOND)=252.430 E(ANGL)=384.260 | | E(DIHE)=0.000 E(IMPR)=100.277 E(VDW )=-240.864 E(ELEC)=-143.029 | | E(CDIH)=6.544 E(NOE )=249.683 E(PLAN)=12.528 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 66080 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66063 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 65939 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65848 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65845 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65826 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 65821 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=1216.333 E(kin)=588.891 temperature=291.820 | | Etotal =627.442 grad(E)=67.328 E(BOND)=230.799 E(ANGL)=414.143 | | E(DIHE)=0.000 E(IMPR)=86.583 E(VDW )=-228.533 E(ELEC)=-136.119 | | E(CDIH)=8.173 E(NOE )=236.241 E(PLAN)=16.155 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65844 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65880 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65912 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65934 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66009 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 66094 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=1217.240 E(kin)=609.646 temperature=302.105 | | Etotal =607.594 grad(E)=66.592 E(BOND)=243.587 E(ANGL)=374.911 | | E(DIHE)=0.000 E(IMPR)=94.376 E(VDW )=-230.499 E(ELEC)=-143.971 | | E(CDIH)=6.711 E(NOE )=247.251 E(PLAN)=15.228 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 66248 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 66275 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66236 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.18 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66113 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66139 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66144 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart NBONDS: found 66170 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=1221.851 E(kin)=610.103 temperature=302.332 | | Etotal =611.747 grad(E)=68.181 E(BOND)=241.235 E(ANGL)=399.407 | | E(DIHE)=0.000 E(IMPR)=83.436 E(VDW )=-234.256 E(ELEC)=-145.336 | | E(CDIH)=8.919 E(NOE )=243.228 E(PLAN)=15.113 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66201 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 66223 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66164 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 66127 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 66152 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66170 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=1218.265 E(kin)=620.182 temperature=307.326 | | Etotal =598.083 grad(E)=66.626 E(BOND)=218.168 E(ANGL)=392.509 | | E(DIHE)=0.000 E(IMPR)=98.448 E(VDW )=-234.263 E(ELEC)=-142.442 | | E(CDIH)=6.704 E(NOE )=241.308 E(PLAN)=17.649 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66147 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66207 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 66157 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66080 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66039 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65940 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65844 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65841 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=1227.322 E(kin)=610.636 temperature=302.596 | | Etotal =616.687 grad(E)=69.520 E(BOND)=222.708 E(ANGL)=402.526 | | E(DIHE)=0.000 E(IMPR)=102.626 E(VDW )=-232.570 E(ELEC)=-136.237 | | E(CDIH)=6.542 E(NOE )=237.347 E(PLAN)=13.746 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 65877 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 65874 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65945 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65969 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65931 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65869 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65810 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65587 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=1215.741 E(kin)=596.498 temperature=295.590 | | Etotal =619.243 grad(E)=68.238 E(BOND)=235.202 E(ANGL)=390.532 | | E(DIHE)=0.000 E(IMPR)=103.832 E(VDW )=-239.656 E(ELEC)=-146.312 | | E(CDIH)=6.162 E(NOE )=257.280 E(PLAN)=12.203 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65520 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65469 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65390 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65375 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65344 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65317 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65389 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65469 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=1210.675 E(kin)=617.518 temperature=306.006 | | Etotal =593.156 grad(E)=66.900 E(BOND)=221.578 E(ANGL)=404.188 | | E(DIHE)=0.000 E(IMPR)=88.819 E(VDW )=-240.497 E(ELEC)=-146.933 | | E(CDIH)=12.822 E(NOE )=238.279 E(PLAN)=14.901 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1218.124 E(kin)=605.540 temperature=300.071 | | Etotal =612.583 grad(E)=67.788 E(BOND)=229.137 E(ANGL)=398.232 | | E(DIHE)=0.000 E(IMPR)=96.295 E(VDW )=-236.445 E(ELEC)=-144.183 | | E(CDIH)=7.839 E(NOE )=246.494 E(PLAN)=15.215 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.571 E(kin)=12.740 temperature=6.313 | | Etotal =14.907 grad(E)=1.384 E(BOND)=11.041 E(ANGL)=12.550 | | E(DIHE)=0.000 E(IMPR)=6.713 E(VDW )=7.424 E(ELEC)=3.992 | | E(CDIH)=2.683 E(NOE )=8.845 E(PLAN)=1.464 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=1217.643 E(kin)=605.340 temperature=299.972 | | Etotal =612.303 grad(E)=66.826 E(BOND)=222.986 E(ANGL)=399.676 | | E(DIHE)=0.000 E(IMPR)=95.303 E(VDW )=-234.454 E(ELEC)=-143.378 | | E(CDIH)=8.525 E(NOE )=247.943 E(PLAN)=15.701 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=14.085 E(kin)=13.211 temperature=6.546 | | Etotal =16.681 grad(E)=1.923 E(BOND)=12.080 E(ANGL)=13.669 | | E(DIHE)=0.000 E(IMPR)=7.045 E(VDW )=9.023 E(ELEC)=7.606 | | E(CDIH)=2.953 E(NOE )=9.901 E(PLAN)=2.191 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65449 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart NBONDS: found 65388 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.19 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65379 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65293 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65209 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65150 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 65102 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=1212.367 E(kin)=604.434 temperature=299.522 | | Etotal =607.933 grad(E)=67.321 E(BOND)=229.534 E(ANGL)=402.216 | | E(DIHE)=0.000 E(IMPR)=88.502 E(VDW )=-246.422 E(ELEC)=-148.087 | | E(CDIH)=3.329 E(NOE )=262.892 E(PLAN)=15.969 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65107 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 65014 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 64982 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 65015 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart NBONDS: found 65027 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65031 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.30 A apart NBONDS: found 65090 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart NBONDS: found 65131 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=1217.060 E(kin)=602.250 temperature=298.440 | | Etotal =614.809 grad(E)=66.155 E(BOND)=241.388 E(ANGL)=396.065 | | E(DIHE)=0.000 E(IMPR)=94.020 E(VDW )=-234.826 E(ELEC)=-153.237 | | E(CDIH)=14.078 E(NOE )=242.606 E(PLAN)=14.717 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65100 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 65117 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart NBONDS: found 65099 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart NBONDS: found 65045 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 64983 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64936 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64943 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart NBONDS: found 64908 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64823 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=1222.448 E(kin)=575.612 temperature=285.240 | | Etotal =646.836 grad(E)=69.470 E(BOND)=232.708 E(ANGL)=418.853 | | E(DIHE)=0.000 E(IMPR)=111.917 E(VDW )=-232.813 E(ELEC)=-139.336 | | E(CDIH)=6.436 E(NOE )=232.858 E(PLAN)=16.214 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64696 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64696 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64687 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 64622 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64605 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64590 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64535 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.20 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64510 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=1216.861 E(kin)=589.459 temperature=292.102 | | Etotal =627.402 grad(E)=66.921 E(BOND)=244.293 E(ANGL)=397.529 | | E(DIHE)=0.000 E(IMPR)=97.554 E(VDW )=-227.426 E(ELEC)=-139.623 | | E(CDIH)=5.501 E(NOE )=232.265 E(PLAN)=17.308 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64500 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart NBONDS: found 64527 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 64613 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 64635 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64640 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 64612 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=1215.756 E(kin)=618.450 temperature=306.468 | | Etotal =597.306 grad(E)=66.170 E(BOND)=221.678 E(ANGL)=387.606 | | E(DIHE)=0.000 E(IMPR)=94.548 E(VDW )=-229.360 E(ELEC)=-150.653 | | E(CDIH)=11.082 E(NOE )=245.945 E(PLAN)=16.459 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64618 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64571 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 64560 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.22 A apart NBONDS: found 64531 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 64497 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64502 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=1210.520 E(kin)=607.044 temperature=300.816 | | Etotal =603.476 grad(E)=67.247 E(BOND)=208.462 E(ANGL)=396.379 | | E(DIHE)=0.000 E(IMPR)=98.019 E(VDW )=-230.462 E(ELEC)=-142.701 | | E(CDIH)=4.733 E(NOE )=252.768 E(PLAN)=16.278 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.31 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64567 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 64647 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64757 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64856 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64958 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.23 A apart NBONDS: found 65005 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart NBONDS: found 64979 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=1224.323 E(kin)=612.267 temperature=303.404 | | Etotal =612.056 grad(E)=67.736 E(BOND)=226.099 E(ANGL)=395.897 | | E(DIHE)=0.000 E(IMPR)=87.375 E(VDW )=-241.900 E(ELEC)=-145.711 | | E(CDIH)=9.413 E(NOE )=262.622 E(PLAN)=18.260 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64925 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64873 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64711 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64552 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart NBONDS: found 64566 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.21 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64553 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=1201.339 E(kin)=611.983 temperature=303.263 | | Etotal =589.357 grad(E)=68.149 E(BOND)=226.013 E(ANGL)=389.305 | | E(DIHE)=0.000 E(IMPR)=91.597 E(VDW )=-231.447 E(ELEC)=-144.773 | | E(CDIH)=7.984 E(NOE )=237.231 E(PLAN)=13.448 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.24 A apart NBONDS: found 64601 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.26 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 64638 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.25 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 64721 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64724 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64793 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64807 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=1234.299 E(kin)=620.624 temperature=307.545 | | Etotal =613.675 grad(E)=68.444 E(BOND)=231.936 E(ANGL)=399.275 | | E(DIHE)=0.000 E(IMPR)=92.331 E(VDW )=-227.826 E(ELEC)=-151.594 | | E(CDIH)=12.676 E(NOE )=242.082 E(PLAN)=14.794 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.36 A apart NBONDS: found 64790 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart NBONDS: found 64806 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64771 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -11 -ADE -H5''" only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 64759 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 64720 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.29 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 64676 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=1234.659 E(kin)=599.367 temperature=297.011 | | Etotal =635.292 grad(E)=69.697 E(BOND)=241.273 E(ANGL)=404.477 | | E(DIHE)=0.000 E(IMPR)=101.163 E(VDW )=-224.780 E(ELEC)=-137.480 | | E(CDIH)=4.278 E(NOE )=229.154 E(PLAN)=17.206 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1219.013 E(kin)=605.371 temperature=299.987 | | Etotal =613.642 grad(E)=67.700 E(BOND)=227.969 E(ANGL)=400.952 | | E(DIHE)=0.000 E(IMPR)=94.937 E(VDW )=-232.981 E(ELEC)=-145.236 | | E(CDIH)=8.487 E(NOE )=243.489 E(PLAN)=16.025 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.465 E(kin)=12.898 temperature=6.392 | | Etotal =14.928 grad(E)=1.401 E(BOND)=10.330 E(ANGL)=12.744 | | E(DIHE)=0.000 E(IMPR)=6.694 E(VDW )=7.637 E(ELEC)=5.271 | | E(CDIH)=2.957 E(NOE )=9.093 E(PLAN)=1.911 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=1217.729 E(kin)=605.342 temperature=299.973 | | Etotal =612.387 grad(E)=66.881 E(BOND)=223.297 E(ANGL)=399.756 | | E(DIHE)=0.000 E(IMPR)=95.280 E(VDW )=-234.362 E(ELEC)=-143.494 | | E(CDIH)=8.523 E(NOE )=247.665 E(PLAN)=15.721 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=13.805 E(kin)=13.191 temperature=6.537 | | Etotal =16.580 grad(E)=1.907 E(BOND)=12.039 E(ANGL)=13.616 | | E(DIHE)=0.000 E(IMPR)=7.024 E(VDW )=8.949 E(ELEC)=7.495 | | E(CDIH)=2.953 E(NOE )=9.912 E(PLAN)=2.176 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.05120 0.01489 -0.00913 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 00:19:05 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 -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66387 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66380 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.28 A apart NBONDS: found 66381 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.27 A apart NBONDS: found 66381 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =41.842 grad(E)=10.319 E(BOND)=27.881 E(ANGL)=155.150 | | E(DIHE)=0.000 E(IMPR)=18.291 E(VDW )=-246.865 E(ELEC)=-143.398 | | E(CDIH)=5.188 E(NOE )=211.815 E(PLAN)=13.780 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =12.825 grad(E)=3.877 E(BOND)=17.559 E(ANGL)=141.660 | | E(DIHE)=0.000 E(IMPR)=18.222 E(VDW )=-250.533 E(ELEC)=-145.550 | | E(CDIH)=5.330 E(NOE )=213.278 E(PLAN)=12.859 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =6.154 grad(E)=2.248 E(BOND)=17.643 E(ANGL)=138.596 | | E(DIHE)=0.000 E(IMPR)=17.356 E(VDW )=-251.635 E(ELEC)=-147.843 | | E(CDIH)=5.393 E(NOE )=214.762 E(PLAN)=11.883 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =3.955 grad(E)=1.426 E(BOND)=17.794 E(ANGL)=138.377 | | E(DIHE)=0.000 E(IMPR)=16.913 E(VDW )=-250.875 E(ELEC)=-149.877 | | E(CDIH)=5.385 E(NOE )=214.735 E(PLAN)=11.504 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =2.089 grad(E)=0.968 E(BOND)=17.748 E(ANGL)=138.349 | | E(DIHE)=0.000 E(IMPR)=16.758 E(VDW )=-251.048 E(ELEC)=-151.707 | | E(CDIH)=5.305 E(NOE )=215.723 E(PLAN)=10.961 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =0.936 grad(E)=1.363 E(BOND)=17.602 E(ANGL)=138.523 | | E(DIHE)=0.000 E(IMPR)=16.695 E(VDW )=-251.143 E(ELEC)=-152.907 | | E(CDIH)=5.332 E(NOE )=215.956 E(PLAN)=10.877 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =-0.058 grad(E)=1.349 E(BOND)=17.604 E(ANGL)=138.378 | | E(DIHE)=0.000 E(IMPR)=17.046 E(VDW )=-250.292 E(ELEC)=-154.265 | | E(CDIH)=5.257 E(NOE )=215.113 E(PLAN)=11.101 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =-0.691 grad(E)=0.911 E(BOND)=17.419 E(ANGL)=138.517 | | E(DIHE)=0.000 E(IMPR)=16.985 E(VDW )=-249.783 E(ELEC)=-155.397 | | E(CDIH)=5.216 E(NOE )=214.993 E(PLAN)=11.358 | ------------------------------------------------------------------------------- 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 $RMS_BOND set to 0.331479E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (A 9 C4' |A 9 C3' |A 9 O3' ) 116.539 110.500 6.039 4.945 445.032 (A 9 C2' |A 9 C3' |A 9 O3' ) 105.955 111.000 -5.045 2.975 383.726 (A 10 C4' |A 10 C3' |A 10 O3' ) 116.094 110.500 5.594 4.243 445.032 (A 9 O3' |A 10 P |A 10 O2P ) 113.612 108.300 5.312 2.525 293.791 Number of violations greater 5.000: 4 RMS deviation= 0.798 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.798054 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 4.00000 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.395 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.395005 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 9 URI H2' set-j-atoms A 11 ADE H8 R= 4.415 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.415 E(NOE)= 17.246 ======================================== set-i-atoms A 10 CYT H1' set-j-atoms A 11 ADE H8 R= 2.328 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.672 E(NOE)= 45.151 ======================================== set-i-atoms A 10 CYT H2' set-j-atoms A 11 ADE H8 R= 3.354 NOE= 2.40 (- 0.60/+ 0.60) Delta= -0.354 E(NOE)= 12.539 ======================================== set-i-atoms A 10 CYT H3' set-j-atoms A 11 ADE H8 R= 3.891 NOE= 2.40 (- 0.60/+ 0.60) Delta= -0.891 E(NOE)= 79.392 ======================================== set-i-atoms A 10 CYT H4' set-j-atoms A 11 ADE H8 R= 2.340 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.660 E(NOE)= 43.547 NOEPRI: RMS diff. = 0.048, #(violat.> 0.2)= 5 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.048, #(viol.> 0.2)= 5 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.481325E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 5.00000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 0 RMS deviation= 0.325 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.324722 (real) X-PLOR>evaluate ($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 17.4186, angle 138.517, dihedral 0, improper 16.9854, NOE 214.993, c-dihedral 5.2163, planar 11.3582, VdW -249.783, elec -155.397, total -0.691197 RMSD: bond 3.314792E-03, angle 0.798054, dihedral 0, improper 0.395005, NOE 4.813252E-02, c-dihedral 0.324722 Violations: bond 0, angle 4, 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= 136482 current use= 0 X-PLOR: total CPU time= 2906.4968 s X-PLOR: entry time at 00:18:34 17-Aug-96 X-PLOR: exit time at 01:07:19 17-Aug-96