X-PLOR: V3.840 user: on: Alpha/OSF at: 16-Aug-96 21:44:21 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=3536.68551635742 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 16:32:32 created by user: COOR>ATOM 1 P GUA A 1 -8.547 10.714 0.020 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -9.201 9.670 -0.809 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 -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62876 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =-192.799 grad(E)=3.867 E(BOND)=8.617 E(ANGL)=83.200 | | E(DIHE)=0.000 E(IMPR)=13.440 E(VDW )=-258.722 E(ELEC)=-81.484 | | E(CDIH)=0.174 E(NOE )=33.373 E(PLAN)=8.603 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =-206.407 grad(E)=2.675 E(BOND)=7.263 E(ANGL)=82.314 | | E(DIHE)=0.000 E(IMPR)=11.202 E(VDW )=-266.497 E(ELEC)=-83.589 | | E(CDIH)=0.136 E(NOE )=32.779 E(PLAN)=9.985 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =-214.593 grad(E)=2.932 E(BOND)=5.755 E(ANGL)=78.240 | | E(DIHE)=0.000 E(IMPR)=12.404 E(VDW )=-267.045 E(ELEC)=-86.187 | | E(CDIH)=0.319 E(NOE )=31.968 E(PLAN)=9.953 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =-222.509 grad(E)=2.778 E(BOND)=7.251 E(ANGL)=77.900 | | E(DIHE)=0.000 E(IMPR)=12.782 E(VDW )=-271.138 E(ELEC)=-92.294 | | E(CDIH)=0.356 E(NOE )=32.695 E(PLAN)=9.939 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =-230.047 grad(E)=2.942 E(BOND)=7.992 E(ANGL)=79.589 | | E(DIHE)=0.000 E(IMPR)=13.179 E(VDW )=-274.540 E(ELEC)=-99.917 | | E(CDIH)=0.310 E(NOE )=33.113 E(PLAN)=10.226 | ------------------------------------------------------------------------------- NBONDS: found 63132 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =-235.883 grad(E)=2.189 E(BOND)=7.559 E(ANGL)=79.762 | | E(DIHE)=0.000 E(IMPR)=13.359 E(VDW )=-276.072 E(ELEC)=-106.860 | | E(CDIH)=0.281 E(NOE )=35.156 E(PLAN)=10.932 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =-238.722 grad(E)=1.886 E(BOND)=7.854 E(ANGL)=79.532 | | E(DIHE)=0.000 E(IMPR)=13.933 E(VDW )=-276.481 E(ELEC)=-110.519 | | E(CDIH)=0.365 E(NOE )=35.367 E(PLAN)=11.226 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =-241.521 grad(E)=2.098 E(BOND)=7.925 E(ANGL)=79.616 | | E(DIHE)=0.000 E(IMPR)=13.847 E(VDW )=-277.366 E(ELEC)=-114.050 | | E(CDIH)=0.489 E(NOE )=36.523 E(PLAN)=11.496 | ------------------------------------------------------------------------------- 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= 0.116279386E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.05645 0.04692 0.01980 velocity [A/ps] : 0.25597 0.48005 0.22770 ang. mom. [amu A/ps] : 4474.38802 1436.59081 -36111.23037 kin. ener. [Kcal/mol] : 2.80355 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.05645 0.04692 0.01980 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)=346.811 E(kin)=588.332 temperature=291.543 | | Etotal =-241.521 grad(E)=2.098 E(BOND)=7.925 E(ANGL)=79.616 | | E(DIHE)=0.000 E(IMPR)=13.847 E(VDW )=-277.366 E(ELEC)=-114.050 | | E(CDIH)=0.489 E(NOE )=36.523 E(PLAN)=11.496 | ------------------------------------------------------------------------------- NBONDS: found 63302 intra-atom interactions NBONDS: found 63249 intra-atom interactions NBONDS: found 63266 intra-atom interactions NBONDS: found 63259 intra-atom interactions NBONDS: found 63234 intra-atom interactions NBONDS: found 63174 intra-atom interactions NBONDS: found 63128 intra-atom interactions NBONDS: found 63133 intra-atom interactions NBONDS: found 63106 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" NBONDS: found 63123 intra-atom interactions NBONDS: found 63130 intra-atom interactions NBONDS: found 63162 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=953.976 E(kin)=591.874 temperature=293.298 | | Etotal =362.102 grad(E)=67.104 E(BOND)=220.702 E(ANGL)=342.573 | | E(DIHE)=0.000 E(IMPR)=82.388 E(VDW )=-263.406 E(ELEC)=-106.169 | | E(CDIH)=1.266 E(NOE )=70.087 E(PLAN)=14.661 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63168 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 63346 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 63403 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63378 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 63378 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63446 intra-atom interactions NBONDS: found 63414 intra-atom interactions NBONDS: found 63370 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=934.379 E(kin)=597.192 temperature=295.934 | | Etotal =337.187 grad(E)=63.028 E(BOND)=198.331 E(ANGL)=333.296 | | E(DIHE)=0.000 E(IMPR)=94.437 E(VDW )=-251.726 E(ELEC)=-130.920 | | E(CDIH)=5.440 E(NOE )=73.051 E(PLAN)=15.277 | ------------------------------------------------------------------------------- NBONDS: found 63385 intra-atom interactions NBONDS: found 63324 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63215 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 63142 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63054 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62949 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62906 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62787 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62710 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=928.227 E(kin)=627.590 temperature=310.997 | | Etotal =300.638 grad(E)=61.158 E(BOND)=194.474 E(ANGL)=323.985 | | E(DIHE)=0.000 E(IMPR)=83.395 E(VDW )=-257.125 E(ELEC)=-123.007 | | E(CDIH)=2.100 E(NOE )=59.897 E(PLAN)=16.919 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62523 intra-atom interactions NBONDS: found 62385 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62460 intra-atom interactions NBONDS: found 62557 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62610 intra-atom interactions NBONDS: found 62665 intra-atom interactions NBONDS: found 62784 intra-atom interactions NBONDS: found 62852 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=939.102 E(kin)=576.516 temperature=285.688 | | Etotal =362.586 grad(E)=66.706 E(BOND)=206.107 E(ANGL)=359.047 | | E(DIHE)=0.000 E(IMPR)=91.301 E(VDW )=-266.950 E(ELEC)=-132.061 | | E(CDIH)=2.805 E(NOE )=88.338 E(PLAN)=13.998 | ------------------------------------------------------------------------------- NBONDS: found 62969 intra-atom interactions NBONDS: found 63031 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 63017 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 63012 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 63008 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62995 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62928 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=948.214 E(kin)=602.027 temperature=298.330 | | Etotal =346.187 grad(E)=64.085 E(BOND)=200.381 E(ANGL)=338.188 | | E(DIHE)=0.000 E(IMPR)=91.276 E(VDW )=-250.783 E(ELEC)=-120.731 | | E(CDIH)=2.517 E(NOE )=70.171 E(PLAN)=15.168 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62799 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62714 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62655 intra-atom interactions NBONDS: found 62608 intra-atom interactions NBONDS: found 62578 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62571 intra-atom interactions NBONDS: found 62564 intra-atom interactions NBONDS: found 62529 intra-atom interactions NBONDS: found 62539 intra-atom interactions NBONDS: found 62594 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=972.035 E(kin)=588.832 temperature=291.791 | | Etotal =383.203 grad(E)=67.365 E(BOND)=227.223 E(ANGL)=355.620 | | E(DIHE)=0.000 E(IMPR)=91.582 E(VDW )=-253.981 E(ELEC)=-116.139 | | E(CDIH)=0.846 E(NOE )=63.450 E(PLAN)=14.602 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62658 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62781 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62855 intra-atom interactions NBONDS: found 62889 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62903 intra-atom interactions NBONDS: found 62876 intra-atom interactions NBONDS: found 62851 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62826 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62845 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=936.814 E(kin)=604.447 temperature=299.529 | | Etotal =332.367 grad(E)=66.872 E(BOND)=217.711 E(ANGL)=319.201 | | E(DIHE)=0.000 E(IMPR)=90.585 E(VDW )=-260.824 E(ELEC)=-136.915 | | E(CDIH)=1.254 E(NOE )=83.811 E(PLAN)=17.544 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62855 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62845 intra-atom interactions NBONDS: found 62842 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62787 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62700 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62701 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62690 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62699 intra-atom interactions NBONDS: found 62823 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=928.738 E(kin)=622.642 temperature=308.545 | | Etotal =306.096 grad(E)=64.150 E(BOND)=172.658 E(ANGL)=327.689 | | E(DIHE)=0.000 E(IMPR)=101.857 E(VDW )=-260.600 E(ELEC)=-136.823 | | E(CDIH)=1.808 E(NOE )=80.765 E(PLAN)=18.743 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62965 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 63046 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 63162 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63291 intra-atom interactions NBONDS: found 63348 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63431 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 63558 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.41 A apart NBONDS: found 63593 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=968.416 E(kin)=609.940 temperature=302.251 | | Etotal =358.476 grad(E)=67.146 E(BOND)=196.534 E(ANGL)=351.916 | | E(DIHE)=0.000 E(IMPR)=99.747 E(VDW )=-242.108 E(ELEC)=-132.695 | | E(CDIH)=2.568 E(NOE )=66.627 E(PLAN)=15.886 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 63608 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 63672 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63662 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 63661 intra-atom interactions NBONDS: found 63659 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63594 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63526 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 63427 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 63305 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=917.930 E(kin)=615.478 temperature=304.995 | | Etotal =302.453 grad(E)=63.965 E(BOND)=194.635 E(ANGL)=331.560 | | E(DIHE)=0.000 E(IMPR)=85.414 E(VDW )=-267.236 E(ELEC)=-126.537 | | E(CDIH)=0.746 E(NOE )=69.090 E(PLAN)=14.780 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=937.514 E(kin)=603.342 temperature=298.982 | | Etotal =334.172 grad(E)=64.771 E(BOND)=202.358 E(ANGL)=332.305 | | E(DIHE)=0.000 E(IMPR)=89.353 E(VDW )=-258.315 E(ELEC)=-124.232 | | E(CDIH)=2.241 E(NOE )=74.773 E(PLAN)=15.690 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=42.058 E(kin)=21.637 temperature=10.722 | | Etotal =29.670 grad(E)=1.975 E(BOND)=12.396 E(ANGL)=15.340 | | E(DIHE)=0.000 E(IMPR)=8.102 E(VDW )=7.765 E(ELEC)=8.245 | | E(CDIH)=1.436 E(NOE )=8.133 E(PLAN)=1.867 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63231 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 63162 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 63087 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63042 intra-atom interactions NBONDS: found 63043 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63065 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63017 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63023 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 63079 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63163 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=941.613 E(kin)=579.918 temperature=287.374 | | Etotal =361.696 grad(E)=67.461 E(BOND)=216.980 E(ANGL)=352.765 | | E(DIHE)=0.000 E(IMPR)=89.618 E(VDW )=-271.402 E(ELEC)=-111.657 | | E(CDIH)=1.796 E(NOE )=71.786 E(PLAN)=11.810 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 63194 intra-atom interactions NBONDS: found 63208 intra-atom interactions NBONDS: found 63204 intra-atom interactions NBONDS: found 63200 intra-atom interactions NBONDS: found 63178 intra-atom interactions NBONDS: found 63163 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63116 intra-atom interactions NBONDS: found 63120 intra-atom interactions NBONDS: found 63123 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 63084 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 63009 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=942.636 E(kin)=597.948 temperature=296.308 | | Etotal =344.688 grad(E)=65.397 E(BOND)=207.784 E(ANGL)=352.710 | | E(DIHE)=0.000 E(IMPR)=79.011 E(VDW )=-257.496 E(ELEC)=-121.086 | | E(CDIH)=0.865 E(NOE )=65.016 E(PLAN)=17.884 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62842 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62743 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62687 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62635 intra-atom interactions NBONDS: found 62619 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62585 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62587 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=927.874 E(kin)=594.227 temperature=294.464 | | Etotal =333.647 grad(E)=68.039 E(BOND)=216.366 E(ANGL)=328.921 | | E(DIHE)=0.000 E(IMPR)=84.750 E(VDW )=-257.223 E(ELEC)=-132.666 | | E(CDIH)=5.480 E(NOE )=68.030 E(PLAN)=19.989 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62515 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62395 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62287 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62215 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62124 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62051 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61974 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62027 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=942.015 E(kin)=604.639 temperature=299.624 | | Etotal =337.376 grad(E)=65.333 E(BOND)=198.582 E(ANGL)=337.953 | | E(DIHE)=0.000 E(IMPR)=89.325 E(VDW )=-257.233 E(ELEC)=-124.402 | | E(CDIH)=4.426 E(NOE )=70.118 E(PLAN)=18.608 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62038 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62046 intra-atom interactions NBONDS: found 62132 intra-atom interactions NBONDS: found 62182 intra-atom interactions NBONDS: found 62197 intra-atom interactions NBONDS: found 62211 intra-atom interactions NBONDS: found 62127 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=965.851 E(kin)=602.822 temperature=298.724 | | Etotal =363.029 grad(E)=66.707 E(BOND)=195.819 E(ANGL)=346.743 | | E(DIHE)=0.000 E(IMPR)=113.362 E(VDW )=-262.604 E(ELEC)=-130.091 | | E(CDIH)=1.184 E(NOE )=82.611 E(PLAN)=16.005 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62087 intra-atom interactions NBONDS: found 62067 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62004 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61965 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61950 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61955 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61950 intra-atom interactions NBONDS: found 61990 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=919.155 E(kin)=614.286 temperature=304.405 | | Etotal =304.869 grad(E)=64.889 E(BOND)=199.595 E(ANGL)=304.346 | | E(DIHE)=0.000 E(IMPR)=105.000 E(VDW )=-265.332 E(ELEC)=-122.906 | | E(CDIH)=1.315 E(NOE )=70.816 E(PLAN)=12.036 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62048 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62083 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62147 intra-atom interactions NBONDS: found 62226 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62252 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62257 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62307 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62373 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62459 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62500 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=934.320 E(kin)=610.252 temperature=302.405 | | Etotal =324.068 grad(E)=67.064 E(BOND)=205.264 E(ANGL)=329.714 | | E(DIHE)=0.000 E(IMPR)=91.816 E(VDW )=-258.640 E(ELEC)=-125.703 | | E(CDIH)=4.509 E(NOE )=60.451 E(PLAN)=16.656 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62546 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62486 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62498 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62459 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62378 intra-atom interactions NBONDS: found 62323 intra-atom interactions NBONDS: found 62269 intra-atom interactions NBONDS: found 62219 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62189 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62157 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=924.754 E(kin)=595.864 temperature=295.276 | | Etotal =328.890 grad(E)=64.124 E(BOND)=199.596 E(ANGL)=350.328 | | E(DIHE)=0.000 E(IMPR)=91.673 E(VDW )=-252.383 E(ELEC)=-137.787 | | E(CDIH)=3.263 E(NOE )=57.688 E(PLAN)=16.512 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62159 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62141 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62078 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62035 intra-atom interactions NBONDS: found 62056 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61983 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61973 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 61989 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61977 intra-atom interactions NBONDS: found 61975 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61960 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=938.354 E(kin)=605.019 temperature=299.812 | | Etotal =333.335 grad(E)=65.409 E(BOND)=202.581 E(ANGL)=339.376 | | E(DIHE)=0.000 E(IMPR)=92.029 E(VDW )=-242.271 E(ELEC)=-133.133 | | E(CDIH)=1.516 E(NOE )=56.256 E(PLAN)=16.980 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61897 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61818 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61748 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61724 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61673 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61635 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61551 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.46 A apart NBONDS: found 61579 intra-atom interactions NBONDS: found 61523 intra-atom interactions NBONDS: found 61435 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=933.643 E(kin)=610.657 temperature=302.606 | | Etotal =322.986 grad(E)=65.418 E(BOND)=198.748 E(ANGL)=329.062 | | E(DIHE)=0.000 E(IMPR)=97.921 E(VDW )=-255.845 E(ELEC)=-129.435 | | E(CDIH)=2.714 E(NOE )=65.705 E(PLAN)=14.115 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=932.670 E(kin)=605.418 temperature=300.010 | | Etotal =327.251 grad(E)=65.060 E(BOND)=204.734 E(ANGL)=332.467 | | E(DIHE)=0.000 E(IMPR)=90.663 E(VDW )=-259.000 E(ELEC)=-127.910 | | E(CDIH)=2.192 E(NOE )=68.288 E(PLAN)=15.817 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=13.676 E(kin)=12.579 temperature=6.233 | | Etotal =18.168 grad(E)=1.548 E(BOND)=9.871 E(ANGL)=11.989 | | E(DIHE)=0.000 E(IMPR)=7.478 E(VDW )=5.769 E(ELEC)=7.439 | | E(CDIH)=1.573 E(NOE )=7.576 E(PLAN)=2.125 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=935.092 E(kin)=604.380 temperature=299.496 | | Etotal =330.712 grad(E)=64.915 E(BOND)=203.546 E(ANGL)=332.386 | | E(DIHE)=0.000 E(IMPR)=90.008 E(VDW )=-258.658 E(ELEC)=-126.071 | | E(CDIH)=2.216 E(NOE )=71.531 E(PLAN)=15.753 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=31.366 E(kin)=17.728 temperature=8.785 | | Etotal =24.843 grad(E)=1.780 E(BOND)=11.268 E(ANGL)=13.767 | | E(DIHE)=0.000 E(IMPR)=7.824 E(VDW )=6.849 E(ELEC)=8.065 | | E(CDIH)=1.506 E(NOE )=8.502 E(PLAN)=2.001 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 61408 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.45 A apart NBONDS: found 61342 intra-atom interactions NBONDS: found 61295 intra-atom interactions NBONDS: found 61277 intra-atom interactions NBONDS: found 61335 intra-atom interactions NBONDS: found 61345 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61496 intra-atom interactions NBONDS: found 61615 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=924.536 E(kin)=614.129 temperature=304.326 | | Etotal =310.408 grad(E)=64.043 E(BOND)=185.945 E(ANGL)=338.852 | | E(DIHE)=0.000 E(IMPR)=92.183 E(VDW )=-255.458 E(ELEC)=-137.995 | | E(CDIH)=2.553 E(NOE )=65.949 E(PLAN)=18.380 | ------------------------------------------------------------------------------- NBONDS: found 61743 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.48 A apart NBONDS: found 61832 intra-atom interactions NBONDS: found 61880 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61974 intra-atom interactions NBONDS: found 62048 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.44 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart NBONDS: found 62060 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.38 A apart NBONDS: found 62111 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62133 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=957.303 E(kin)=598.160 temperature=296.413 | | Etotal =359.142 grad(E)=67.297 E(BOND)=220.442 E(ANGL)=348.505 | | E(DIHE)=0.000 E(IMPR)=96.258 E(VDW )=-259.984 E(ELEC)=-123.708 | | E(CDIH)=0.474 E(NOE )=60.600 E(PLAN)=16.554 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.34 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62161 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.43 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.49 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62248 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.39 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62310 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.43 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62304 intra-atom interactions NBONDS: found 62326 intra-atom interactions NBONDS: found 62311 intra-atom interactions NBONDS: found 62336 intra-atom interactions NBONDS: found 62342 intra-atom interactions NBONDS: found 62389 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=926.034 E(kin)=603.544 temperature=299.081 | | Etotal =322.490 grad(E)=65.265 E(BOND)=201.952 E(ANGL)=346.503 | | E(DIHE)=0.000 E(IMPR)=86.720 E(VDW )=-261.155 E(ELEC)=-129.652 | | E(CDIH)=2.486 E(NOE )=58.422 E(PLAN)=17.213 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62380 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62394 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62366 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62378 intra-atom interactions %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.47 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62322 intra-atom interactions %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62256 intra-atom interactions %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62268 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62246 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=925.225 E(kin)=606.373 temperature=300.483 | | Etotal =318.852 grad(E)=64.871 E(BOND)=189.890 E(ANGL)=328.496 | | E(DIHE)=0.000 E(IMPR)=93.421 E(VDW )=-252.864 E(ELEC)=-118.922 | | E(CDIH)=2.544 E(NOE )=61.475 E(PLAN)=14.813 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62311 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.38 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62323 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62394 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62397 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62398 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62441 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62422 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 62425 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=960.169 E(kin)=613.251 temperature=303.892 | | Etotal =346.918 grad(E)=66.497 E(BOND)=208.835 E(ANGL)=354.348 | | E(DIHE)=0.000 E(IMPR)=84.053 E(VDW )=-254.934 E(ELEC)=-123.049 | | E(CDIH)=1.836 E(NOE )=63.048 E(PLAN)=12.779 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62378 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62307 intra-atom interactions NBONDS: found 62234 intra-atom interactions NBONDS: found 62168 intra-atom interactions NBONDS: found 62117 intra-atom interactions NBONDS: found 62096 intra-atom interactions %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62044 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62009 intra-atom interactions %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61986 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61942 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61956 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=929.865 E(kin)=602.586 temperature=298.606 | | Etotal =327.279 grad(E)=66.459 E(BOND)=193.892 E(ANGL)=353.869 | | E(DIHE)=0.000 E(IMPR)=91.113 E(VDW )=-266.514 E(ELEC)=-128.460 | | E(CDIH)=1.328 E(NOE )=65.612 E(PLAN)=16.439 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61949 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61963 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.43 A apart NBONDS: found 61968 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61998 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62024 intra-atom interactions NBONDS: found 62079 intra-atom interactions NBONDS: found 62110 intra-atom interactions NBONDS: found 62097 intra-atom interactions NBONDS: found 62113 intra-atom interactions NBONDS: found 62111 intra-atom interactions NBONDS: found 62124 intra-atom interactions NBONDS: found 62125 intra-atom interactions NBONDS: found 62074 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=932.703 E(kin)=613.511 temperature=304.020 | | Etotal =319.192 grad(E)=65.505 E(BOND)=187.208 E(ANGL)=352.790 | | E(DIHE)=0.000 E(IMPR)=102.614 E(VDW )=-270.261 E(ELEC)=-142.249 | | E(CDIH)=1.299 E(NOE )=71.687 E(PLAN)=16.104 | ------------------------------------------------------------------------------- NBONDS: found 62057 intra-atom interactions NBONDS: found 62037 intra-atom interactions NBONDS: found 62027 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62060 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62097 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62132 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62182 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62243 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62298 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62411 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62481 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=946.528 E(kin)=600.839 temperature=297.741 | | Etotal =345.689 grad(E)=67.409 E(BOND)=215.761 E(ANGL)=327.761 | | E(DIHE)=0.000 E(IMPR)=98.176 E(VDW )=-255.918 E(ELEC)=-139.653 | | E(CDIH)=2.145 E(NOE )=84.984 E(PLAN)=12.433 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62594 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62608 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart NBONDS: found 62632 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62564 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62551 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62486 intra-atom interactions NBONDS: found 62437 intra-atom interactions NBONDS: found 62472 intra-atom interactions NBONDS: found 62499 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=916.373 E(kin)=609.183 temperature=301.876 | | Etotal =307.189 grad(E)=65.394 E(BOND)=212.628 E(ANGL)=314.187 | | E(DIHE)=0.000 E(IMPR)=95.821 E(VDW )=-267.038 E(ELEC)=-126.623 | | E(CDIH)=1.989 E(NOE )=60.955 E(PLAN)=15.269 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62501 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62535 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62565 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62579 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62519 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62559 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62593 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62552 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62565 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62572 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=939.916 E(kin)=587.601 temperature=291.181 | | Etotal =352.315 grad(E)=67.541 E(BOND)=211.413 E(ANGL)=340.001 | | E(DIHE)=0.000 E(IMPR)=102.785 E(VDW )=-254.138 E(ELEC)=-135.923 | | E(CDIH)=3.486 E(NOE )=66.318 E(PLAN)=18.374 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=929.867 E(kin)=605.449 temperature=300.026 | | Etotal =324.418 grad(E)=65.841 E(BOND)=204.119 E(ANGL)=333.914 | | E(DIHE)=0.000 E(IMPR)=95.252 E(VDW )=-260.216 E(ELEC)=-130.677 | | E(CDIH)=2.329 E(NOE )=64.369 E(PLAN)=15.329 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=13.625 E(kin)=12.883 temperature=6.384 | | Etotal =18.368 grad(E)=1.672 E(BOND)=9.869 E(ANGL)=11.878 | | E(DIHE)=0.000 E(IMPR)=6.497 E(VDW )=6.145 E(ELEC)=6.479 | | E(CDIH)=1.577 E(NOE )=7.412 E(PLAN)=1.578 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=933.350 E(kin)=604.737 temperature=299.672 | | Etotal =328.614 grad(E)=65.224 E(BOND)=203.737 E(ANGL)=332.895 | | E(DIHE)=0.000 E(IMPR)=91.756 E(VDW )=-259.177 E(ELEC)=-127.607 | | E(CDIH)=2.254 E(NOE )=69.143 E(PLAN)=15.612 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=26.904 E(kin)=16.281 temperature=8.068 | | Etotal =23.081 grad(E)=1.799 E(BOND)=10.825 E(ANGL)=13.187 | | E(DIHE)=0.000 E(IMPR)=7.809 E(VDW )=6.663 E(ELEC)=7.878 | | E(CDIH)=1.531 E(NOE )=8.826 E(PLAN)=1.881 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62634 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62612 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62596 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62564 intra-atom interactions NBONDS: found 62545 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62585 intra-atom interactions NBONDS: found 62609 intra-atom interactions NBONDS: found 62759 intra-atom interactions NBONDS: found 62832 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=946.042 E(kin)=597.740 temperature=296.205 | | Etotal =348.302 grad(E)=64.279 E(BOND)=206.053 E(ANGL)=345.497 | | E(DIHE)=0.000 E(IMPR)=95.302 E(VDW )=-259.128 E(ELEC)=-131.854 | | E(CDIH)=3.149 E(NOE )=72.103 E(PLAN)=17.181 | ------------------------------------------------------------------------------- NBONDS: found 62928 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 63007 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62982 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62956 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62941 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62894 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62855 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62801 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62830 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62761 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=946.674 E(kin)=613.308 temperature=303.920 | | Etotal =333.366 grad(E)=65.220 E(BOND)=205.197 E(ANGL)=344.676 | | E(DIHE)=0.000 E(IMPR)=86.463 E(VDW )=-261.013 E(ELEC)=-127.489 | | E(CDIH)=0.721 E(NOE )=70.687 E(PLAN)=14.123 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62754 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62734 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62783 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62822 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62831 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62897 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62894 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=944.598 E(kin)=605.542 temperature=300.072 | | Etotal =339.056 grad(E)=66.432 E(BOND)=213.316 E(ANGL)=338.787 | | E(DIHE)=0.000 E(IMPR)=95.829 E(VDW )=-248.273 E(ELEC)=-141.881 | | E(CDIH)=2.243 E(NOE )=66.381 E(PLAN)=12.652 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62821 intra-atom interactions NBONDS: found 62852 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62796 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62822 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62809 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62770 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62822 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62862 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=937.017 E(kin)=613.087 temperature=303.810 | | Etotal =323.930 grad(E)=63.685 E(BOND)=197.541 E(ANGL)=334.100 | | E(DIHE)=0.000 E(IMPR)=85.893 E(VDW )=-256.949 E(ELEC)=-137.633 | | E(CDIH)=0.190 E(NOE )=84.319 E(PLAN)=16.470 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62883 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62986 intra-atom interactions NBONDS: found 63038 intra-atom interactions NBONDS: found 63041 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 63009 intra-atom interactions NBONDS: found 62972 intra-atom interactions NBONDS: found 62958 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62925 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=942.879 E(kin)=618.836 temperature=306.659 | | Etotal =324.042 grad(E)=65.921 E(BOND)=204.304 E(ANGL)=332.864 | | E(DIHE)=0.000 E(IMPR)=102.946 E(VDW )=-255.202 E(ELEC)=-134.341 | | E(CDIH)=0.983 E(NOE )=60.529 E(PLAN)=11.959 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62821 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62770 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62695 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62651 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62646 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62619 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62552 intra-atom interactions NBONDS: found 62516 intra-atom interactions NBONDS: found 62431 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=935.659 E(kin)=608.965 temperature=301.768 | | Etotal =326.694 grad(E)=62.492 E(BOND)=203.732 E(ANGL)=335.388 | | E(DIHE)=0.000 E(IMPR)=90.637 E(VDW )=-258.661 E(ELEC)=-132.651 | | E(CDIH)=2.970 E(NOE )=70.270 E(PLAN)=15.010 | ------------------------------------------------------------------------------- NBONDS: found 62301 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62206 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62091 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61992 intra-atom interactions NBONDS: found 61871 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61860 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61869 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61893 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61923 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=925.454 E(kin)=602.974 temperature=298.799 | | Etotal =322.481 grad(E)=66.453 E(BOND)=193.651 E(ANGL)=347.226 | | E(DIHE)=0.000 E(IMPR)=93.542 E(VDW )=-263.666 E(ELEC)=-138.341 | | E(CDIH)=0.864 E(NOE )=75.742 E(PLAN)=13.462 | ------------------------------------------------------------------------------- NBONDS: found 61968 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61974 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61986 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61973 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61984 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62038 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62048 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62001 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62042 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=934.576 E(kin)=618.045 temperature=306.267 | | Etotal =316.532 grad(E)=64.916 E(BOND)=212.233 E(ANGL)=320.181 | | E(DIHE)=0.000 E(IMPR)=90.687 E(VDW )=-252.985 E(ELEC)=-128.719 | | E(CDIH)=3.435 E(NOE )=58.075 E(PLAN)=13.625 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62080 intra-atom interactions NBONDS: found 62011 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61976 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61896 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61909 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61915 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61919 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61907 intra-atom interactions NBONDS: found 61895 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61879 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61823 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=936.938 E(kin)=617.773 temperature=306.132 | | Etotal =319.165 grad(E)=66.083 E(BOND)=222.307 E(ANGL)=331.736 | | E(DIHE)=0.000 E(IMPR)=82.668 E(VDW )=-262.648 E(ELEC)=-130.458 | | E(CDIH)=4.660 E(NOE )=54.309 E(PLAN)=16.591 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61771 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61692 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61693 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61617 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61600 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61597 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61575 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61618 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61574 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=946.873 E(kin)=610.172 temperature=302.366 | | Etotal =336.701 grad(E)=69.355 E(BOND)=213.729 E(ANGL)=333.641 | | E(DIHE)=0.000 E(IMPR)=94.918 E(VDW )=-250.924 E(ELEC)=-132.213 | | E(CDIH)=1.739 E(NOE )=60.720 E(PLAN)=15.091 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=935.585 E(kin)=605.456 temperature=300.029 | | Etotal =330.129 grad(E)=66.063 E(BOND)=207.087 E(ANGL)=336.123 | | E(DIHE)=0.000 E(IMPR)=95.619 E(VDW )=-258.258 E(ELEC)=-134.583 | | E(CDIH)=1.769 E(NOE )=66.237 E(PLAN)=16.134 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.299 E(kin)=12.156 temperature=6.024 | | Etotal =14.937 grad(E)=1.530 E(BOND)=9.603 E(ANGL)=10.674 | | E(DIHE)=0.000 E(IMPR)=7.138 E(VDW )=5.409 E(ELEC)=4.662 | | E(CDIH)=1.316 E(NOE )=7.720 E(PLAN)=1.979 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=933.909 E(kin)=604.917 temperature=299.762 | | Etotal =328.992 grad(E)=65.434 E(BOND)=204.575 E(ANGL)=333.702 | | E(DIHE)=0.000 E(IMPR)=92.722 E(VDW )=-258.947 E(ELEC)=-129.351 | | E(CDIH)=2.133 E(NOE )=68.417 E(PLAN)=15.743 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=23.779 E(kin)=15.357 temperature=7.610 | | Etotal =21.348 grad(E)=1.773 E(BOND)=10.632 E(ANGL)=12.683 | | E(DIHE)=0.000 E(IMPR)=7.828 E(VDW )=6.385 E(ELEC)=7.817 | | E(CDIH)=1.495 E(NOE )=8.655 E(PLAN)=1.920 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61599 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61650 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61661 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61720 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61701 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61687 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61670 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61650 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61655 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61597 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61592 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=928.335 E(kin)=586.046 temperature=290.410 | | Etotal =342.289 grad(E)=68.149 E(BOND)=213.529 E(ANGL)=338.276 | | E(DIHE)=0.000 E(IMPR)=98.188 E(VDW )=-256.606 E(ELEC)=-127.446 | | E(CDIH)=6.908 E(NOE )=55.355 E(PLAN)=14.084 | ------------------------------------------------------------------------------- NBONDS: found 61520 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61502 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61506 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61520 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61534 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61579 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61561 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61573 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=925.348 E(kin)=610.489 temperature=302.523 | | Etotal =314.859 grad(E)=66.277 E(BOND)=204.370 E(ANGL)=355.318 | | E(DIHE)=0.000 E(IMPR)=88.600 E(VDW )=-266.785 E(ELEC)=-137.892 | | E(CDIH)=1.500 E(NOE )=57.434 E(PLAN)=12.313 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61628 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61689 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61706 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61772 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61901 intra-atom interactions NBONDS: found 61997 intra-atom interactions NBONDS: found 62116 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=927.401 E(kin)=606.753 temperature=300.672 | | Etotal =320.648 grad(E)=65.604 E(BOND)=211.637 E(ANGL)=346.485 | | E(DIHE)=0.000 E(IMPR)=79.068 E(VDW )=-259.026 E(ELEC)=-133.727 | | E(CDIH)=1.665 E(NOE )=57.705 E(PLAN)=16.841 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62171 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62179 intra-atom interactions NBONDS: found 62160 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62169 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62176 intra-atom interactions NBONDS: found 62074 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62119 intra-atom interactions NBONDS: found 62094 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62126 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=916.933 E(kin)=615.160 temperature=304.838 | | Etotal =301.773 grad(E)=66.652 E(BOND)=214.279 E(ANGL)=326.525 | | E(DIHE)=0.000 E(IMPR)=86.640 E(VDW )=-262.821 E(ELEC)=-143.704 | | E(CDIH)=2.955 E(NOE )=61.779 E(PLAN)=16.119 | ------------------------------------------------------------------------------- NBONDS: found 62170 intra-atom interactions NBONDS: found 62177 intra-atom interactions NBONDS: found 62124 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62196 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62265 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62339 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62396 intra-atom interactions NBONDS: found 62522 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=911.418 E(kin)=596.755 temperature=295.717 | | Etotal =314.663 grad(E)=65.829 E(BOND)=202.317 E(ANGL)=339.796 | | E(DIHE)=0.000 E(IMPR)=99.756 E(VDW )=-266.943 E(ELEC)=-142.705 | | E(CDIH)=3.020 E(NOE )=64.054 E(PLAN)=15.367 | ------------------------------------------------------------------------------- NBONDS: found 62660 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.46 A apart NBONDS: found 62792 intra-atom interactions NBONDS: found 62823 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62837 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.49 A apart NBONDS: found 62829 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 62833 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 62812 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=934.027 E(kin)=609.132 temperature=301.851 | | Etotal =324.894 grad(E)=67.697 E(BOND)=200.991 E(ANGL)=345.513 | | E(DIHE)=0.000 E(IMPR)=101.060 E(VDW )=-259.688 E(ELEC)=-143.121 | | E(CDIH)=1.407 E(NOE )=61.267 E(PLAN)=17.465 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.47 A apart NBONDS: found 62728 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 62632 intra-atom interactions NBONDS: found 62552 intra-atom interactions NBONDS: found 62486 intra-atom interactions NBONDS: found 62454 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62408 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62418 intra-atom interactions NBONDS: found 62473 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=920.290 E(kin)=634.136 temperature=314.241 | | Etotal =286.154 grad(E)=66.383 E(BOND)=196.225 E(ANGL)=316.203 | | E(DIHE)=0.000 E(IMPR)=92.791 E(VDW )=-266.462 E(ELEC)=-132.239 | | E(CDIH)=3.443 E(NOE )=60.412 E(PLAN)=15.781 | ------------------------------------------------------------------------------- NBONDS: found 62502 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62547 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62571 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62613 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62661 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62679 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=927.648 E(kin)=594.624 temperature=294.661 | | Etotal =333.024 grad(E)=66.672 E(BOND)=211.063 E(ANGL)=359.295 | | E(DIHE)=0.000 E(IMPR)=89.908 E(VDW )=-263.420 E(ELEC)=-139.605 | | E(CDIH)=2.024 E(NOE )=59.531 E(PLAN)=14.229 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62718 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62683 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62686 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62672 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62615 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62604 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62511 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62456 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62436 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62368 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=933.699 E(kin)=600.816 temperature=297.729 | | Etotal =332.884 grad(E)=67.248 E(BOND)=214.510 E(ANGL)=340.073 | | E(DIHE)=0.000 E(IMPR)=88.791 E(VDW )=-255.827 E(ELEC)=-138.407 | | E(CDIH)=3.321 E(NOE )=66.902 E(PLAN)=13.520 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62374 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62291 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62318 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62329 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62289 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62365 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62354 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62398 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=928.990 E(kin)=612.190 temperature=303.366 | | Etotal =316.801 grad(E)=65.904 E(BOND)=202.416 E(ANGL)=348.898 | | E(DIHE)=0.000 E(IMPR)=88.070 E(VDW )=-261.226 E(ELEC)=-141.257 | | E(CDIH)=0.576 E(NOE )=64.543 E(PLAN)=14.781 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=928.442 E(kin)=605.559 temperature=300.080 | | Etotal =322.883 grad(E)=66.832 E(BOND)=208.234 E(ANGL)=340.304 | | E(DIHE)=0.000 E(IMPR)=92.233 E(VDW )=-261.719 E(ELEC)=-137.738 | | E(CDIH)=2.420 E(NOE )=63.173 E(PLAN)=15.978 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.923 E(kin)=12.590 temperature=6.239 | | Etotal =15.622 grad(E)=1.566 E(BOND)=9.477 E(ANGL)=11.314 | | E(DIHE)=0.000 E(IMPR)=7.044 E(VDW )=5.120 E(ELEC)=5.177 | | E(CDIH)=1.707 E(NOE )=6.451 E(PLAN)=2.263 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=932.816 E(kin)=605.045 temperature=299.825 | | Etotal =327.771 grad(E)=65.713 E(BOND)=205.307 E(ANGL)=335.022 | | E(DIHE)=0.000 E(IMPR)=92.624 E(VDW )=-259.502 E(ELEC)=-131.028 | | E(CDIH)=2.190 E(NOE )=67.368 E(PLAN)=15.790 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=21.836 E(kin)=14.848 temperature=7.358 | | Etotal =20.479 grad(E)=1.821 E(BOND)=10.514 E(ANGL)=12.699 | | E(DIHE)=0.000 E(IMPR)=7.680 E(VDW )=6.252 E(ELEC)=8.094 | | E(CDIH)=1.544 E(NOE )=8.523 E(PLAN)=1.995 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62365 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62341 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62318 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62301 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62317 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62320 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62268 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62213 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=918.961 E(kin)=589.988 temperature=292.364 | | Etotal =328.973 grad(E)=68.087 E(BOND)=216.367 E(ANGL)=347.798 | | E(DIHE)=0.000 E(IMPR)=86.317 E(VDW )=-260.480 E(ELEC)=-134.907 | | E(CDIH)=4.311 E(NOE )=54.039 E(PLAN)=15.528 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62137 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62123 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62126 intra-atom interactions NBONDS: found 62154 intra-atom interactions NBONDS: found 62152 intra-atom interactions NBONDS: found 62111 intra-atom interactions NBONDS: found 62057 intra-atom interactions NBONDS: found 62083 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=960.413 E(kin)=607.831 temperature=301.206 | | Etotal =352.582 grad(E)=67.703 E(BOND)=215.096 E(ANGL)=349.995 | | E(DIHE)=0.000 E(IMPR)=90.432 E(VDW )=-261.047 E(ELEC)=-126.977 | | E(CDIH)=0.385 E(NOE )=68.677 E(PLAN)=16.021 | ------------------------------------------------------------------------------- NBONDS: found 62088 intra-atom interactions NBONDS: found 62100 intra-atom interactions NBONDS: found 62174 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62291 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62349 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62407 intra-atom interactions NBONDS: found 62405 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=942.901 E(kin)=587.692 temperature=291.226 | | Etotal =355.208 grad(E)=67.462 E(BOND)=218.151 E(ANGL)=354.919 | | E(DIHE)=0.000 E(IMPR)=105.454 E(VDW )=-272.697 E(ELEC)=-131.404 | | E(CDIH)=2.134 E(NOE )=65.436 E(PLAN)=13.216 | ------------------------------------------------------------------------------- NBONDS: found 62509 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62518 intra-atom interactions NBONDS: found 62519 intra-atom interactions NBONDS: found 62555 intra-atom interactions NBONDS: found 62573 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62587 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62636 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62624 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62597 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=936.945 E(kin)=609.491 temperature=302.028 | | Etotal =327.454 grad(E)=66.166 E(BOND)=216.986 E(ANGL)=334.992 | | E(DIHE)=0.000 E(IMPR)=97.253 E(VDW )=-264.519 E(ELEC)=-130.340 | | E(CDIH)=3.650 E(NOE )=54.229 E(PLAN)=15.205 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62588 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62527 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62448 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62427 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62373 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62407 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=933.907 E(kin)=606.284 temperature=300.439 | | Etotal =327.623 grad(E)=67.163 E(BOND)=197.518 E(ANGL)=352.882 | | E(DIHE)=0.000 E(IMPR)=87.629 E(VDW )=-275.418 E(ELEC)=-126.853 | | E(CDIH)=4.592 E(NOE )=67.084 E(PLAN)=20.188 | ------------------------------------------------------------------------------- NBONDS: found 62444 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62458 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62488 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62479 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62485 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62450 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62470 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62456 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62422 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=951.121 E(kin)=600.648 temperature=297.646 | | Etotal =350.473 grad(E)=69.134 E(BOND)=235.710 E(ANGL)=340.358 | | E(DIHE)=0.000 E(IMPR)=87.561 E(VDW )=-273.558 E(ELEC)=-130.793 | | E(CDIH)=0.751 E(NOE )=71.390 E(PLAN)=19.053 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62406 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62377 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62341 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62262 intra-atom interactions NBONDS: found 62228 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62161 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62115 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62101 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62155 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=951.715 E(kin)=625.106 temperature=309.766 | | Etotal =326.609 grad(E)=64.989 E(BOND)=216.159 E(ANGL)=343.814 | | E(DIHE)=0.000 E(IMPR)=83.279 E(VDW )=-270.998 E(ELEC)=-125.686 | | E(CDIH)=0.644 E(NOE )=64.901 E(PLAN)=14.495 | ------------------------------------------------------------------------------- NBONDS: found 62216 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62155 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62121 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62164 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62144 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62184 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62219 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62235 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=933.090 E(kin)=623.813 temperature=309.126 | | Etotal =309.277 grad(E)=64.394 E(BOND)=209.777 E(ANGL)=320.193 | | E(DIHE)=0.000 E(IMPR)=87.626 E(VDW )=-265.369 E(ELEC)=-134.071 | | E(CDIH)=2.050 E(NOE )=74.856 E(PLAN)=14.215 | ------------------------------------------------------------------------------- NBONDS: found 62308 intra-atom interactions NBONDS: found 62355 intra-atom interactions NBONDS: found 62350 intra-atom interactions NBONDS: found 62357 intra-atom interactions NBONDS: found 62335 intra-atom interactions NBONDS: found 62223 intra-atom interactions NBONDS: found 62180 intra-atom interactions NBONDS: found 62092 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=940.411 E(kin)=586.226 temperature=290.500 | | Etotal =354.185 grad(E)=66.725 E(BOND)=215.240 E(ANGL)=358.261 | | E(DIHE)=0.000 E(IMPR)=94.362 E(VDW )=-262.182 E(ELEC)=-130.930 | | E(CDIH)=1.851 E(NOE )=60.720 E(PLAN)=16.863 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62100 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62084 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62063 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62044 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62133 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62223 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62311 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62380 intra-atom interactions NBONDS: found 62450 intra-atom interactions NBONDS: found 62441 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=921.919 E(kin)=615.141 temperature=304.828 | | Etotal =306.778 grad(E)=66.116 E(BOND)=203.264 E(ANGL)=344.496 | | E(DIHE)=0.000 E(IMPR)=75.938 E(VDW )=-264.620 E(ELEC)=-133.536 | | E(CDIH)=1.329 E(NOE )=61.353 E(PLAN)=18.554 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=936.529 E(kin)=605.506 temperature=300.054 | | Etotal =331.023 grad(E)=67.240 E(BOND)=211.188 E(ANGL)=342.451 | | E(DIHE)=0.000 E(IMPR)=92.188 E(VDW )=-265.037 E(ELEC)=-130.813 | | E(CDIH)=2.198 E(NOE )=63.588 E(PLAN)=15.260 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=12.066 E(kin)=12.634 temperature=6.261 | | Etotal =17.087 grad(E)=1.644 E(BOND)=10.610 E(ANGL)=11.537 | | E(DIHE)=0.000 E(IMPR)=7.537 E(VDW )=4.802 E(ELEC)=5.721 | | E(CDIH)=1.481 E(NOE )=7.496 E(PLAN)=1.731 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=933.435 E(kin)=605.122 temperature=299.863 | | Etotal =328.313 grad(E)=65.968 E(BOND)=206.287 E(ANGL)=336.261 | | E(DIHE)=0.000 E(IMPR)=92.551 E(VDW )=-260.424 E(ELEC)=-130.992 | | E(CDIH)=2.191 E(NOE )=66.738 E(PLAN)=15.701 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=20.580 E(kin)=14.503 temperature=7.187 | | Etotal =19.990 grad(E)=1.881 E(BOND)=10.755 E(ANGL)=12.816 | | E(DIHE)=0.000 E(IMPR)=7.658 E(VDW )=6.377 E(ELEC)=7.749 | | E(CDIH)=1.534 E(NOE )=8.479 E(PLAN)=1.964 | ------------------------------------------------------------------------------- NBONDS: found 62444 intra-atom interactions NBONDS: found 62470 intra-atom interactions NBONDS: found 62497 intra-atom interactions NBONDS: found 62476 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62486 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62430 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62375 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62334 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=942.351 E(kin)=600.009 temperature=297.330 | | Etotal =342.342 grad(E)=67.830 E(BOND)=211.079 E(ANGL)=337.211 | | E(DIHE)=0.000 E(IMPR)=85.414 E(VDW )=-256.293 E(ELEC)=-118.304 | | E(CDIH)=1.614 E(NOE )=66.187 E(PLAN)=15.435 | ------------------------------------------------------------------------------- NBONDS: found 62320 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62276 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62196 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62159 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62115 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62048 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61977 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61997 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61950 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=933.114 E(kin)=601.044 temperature=297.842 | | Etotal =332.070 grad(E)=67.993 E(BOND)=205.799 E(ANGL)=345.782 | | E(DIHE)=0.000 E(IMPR)=93.844 E(VDW )=-257.944 E(ELEC)=-132.556 | | E(CDIH)=3.555 E(NOE )=59.404 E(PLAN)=14.185 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61943 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61974 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61935 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61919 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61824 intra-atom interactions NBONDS: found 61825 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61804 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61771 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=944.863 E(kin)=602.235 temperature=298.433 | | Etotal =342.628 grad(E)=69.007 E(BOND)=214.916 E(ANGL)=351.512 | | E(DIHE)=0.000 E(IMPR)=95.351 E(VDW )=-266.558 E(ELEC)=-132.691 | | E(CDIH)=4.152 E(NOE )=59.444 E(PLAN)=16.502 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61758 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61739 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61712 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61689 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61682 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61636 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61564 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61571 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61544 intra-atom interactions NBONDS: found 61525 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=949.643 E(kin)=619.060 temperature=306.770 | | Etotal =330.583 grad(E)=65.471 E(BOND)=227.902 E(ANGL)=351.080 | | E(DIHE)=0.000 E(IMPR)=72.485 E(VDW )=-263.900 E(ELEC)=-131.451 | | E(CDIH)=2.750 E(NOE )=54.341 E(PLAN)=17.376 | ------------------------------------------------------------------------------- NBONDS: found 61484 intra-atom interactions NBONDS: found 61448 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61479 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61570 intra-atom interactions NBONDS: found 61613 intra-atom interactions NBONDS: found 61654 intra-atom interactions NBONDS: found 61803 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61851 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=930.864 E(kin)=595.875 temperature=295.281 | | Etotal =334.988 grad(E)=67.970 E(BOND)=210.191 E(ANGL)=345.473 | | E(DIHE)=0.000 E(IMPR)=92.035 E(VDW )=-264.861 E(ELEC)=-145.918 | | E(CDIH)=3.006 E(NOE )=78.181 E(PLAN)=16.882 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61915 intra-atom interactions NBONDS: found 61967 intra-atom interactions NBONDS: found 61978 intra-atom interactions NBONDS: found 61983 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61986 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62016 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61947 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61965 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 61980 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=925.810 E(kin)=590.099 temperature=292.419 | | Etotal =335.712 grad(E)=68.199 E(BOND)=228.034 E(ANGL)=331.709 | | E(DIHE)=0.000 E(IMPR)=92.458 E(VDW )=-254.125 E(ELEC)=-137.275 | | E(CDIH)=2.610 E(NOE )=56.063 E(PLAN)=16.237 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61951 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61948 intra-atom interactions NBONDS: found 61864 intra-atom interactions NBONDS: found 61843 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61883 intra-atom interactions NBONDS: found 61855 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61915 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61953 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 61905 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=936.978 E(kin)=619.238 temperature=306.858 | | Etotal =317.741 grad(E)=70.548 E(BOND)=205.734 E(ANGL)=342.463 | | E(DIHE)=0.000 E(IMPR)=87.486 E(VDW )=-262.085 E(ELEC)=-138.153 | | E(CDIH)=2.942 E(NOE )=62.316 E(PLAN)=17.038 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61965 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61984 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61952 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61922 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61880 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61841 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61787 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61822 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61799 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=937.690 E(kin)=611.490 temperature=303.019 | | Etotal =326.200 grad(E)=67.213 E(BOND)=209.513 E(ANGL)=332.571 | | E(DIHE)=0.000 E(IMPR)=96.398 E(VDW )=-268.581 E(ELEC)=-139.221 | | E(CDIH)=2.516 E(NOE )=76.104 E(PLAN)=16.901 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61770 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61774 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61792 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61801 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61789 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61820 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61864 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61912 intra-atom interactions NBONDS: found 61892 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=940.437 E(kin)=607.941 temperature=301.260 | | Etotal =332.496 grad(E)=67.027 E(BOND)=211.807 E(ANGL)=334.886 | | E(DIHE)=0.000 E(IMPR)=95.150 E(VDW )=-264.242 E(ELEC)=-125.528 | | E(CDIH)=2.122 E(NOE )=60.905 E(PLAN)=17.396 | ------------------------------------------------------------------------------- NBONDS: found 61956 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61981 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62025 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62130 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62180 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62127 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62030 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=931.649 E(kin)=610.145 temperature=302.352 | | Etotal =321.505 grad(E)=65.759 E(BOND)=199.477 E(ANGL)=339.221 | | E(DIHE)=0.000 E(IMPR)=93.949 E(VDW )=-268.671 E(ELEC)=-129.902 | | E(CDIH)=2.460 E(NOE )=69.758 E(PLAN)=15.213 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=933.311 E(kin)=605.442 temperature=300.022 | | Etotal =327.869 grad(E)=67.680 E(BOND)=213.526 E(ANGL)=336.632 | | E(DIHE)=0.000 E(IMPR)=91.346 E(VDW )=-262.274 E(ELEC)=-133.830 | | E(CDIH)=2.013 E(NOE )=63.893 E(PLAN)=16.564 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.364 E(kin)=12.450 temperature=6.169 | | Etotal =15.804 grad(E)=1.729 E(BOND)=9.983 E(ANGL)=11.935 | | E(DIHE)=0.000 E(IMPR)=7.047 E(VDW )=4.843 E(ELEC)=6.413 | | E(CDIH)=1.400 E(NOE )=7.097 E(PLAN)=1.808 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=933.417 E(kin)=605.168 temperature=299.886 | | Etotal =328.249 grad(E)=66.212 E(BOND)=207.321 E(ANGL)=336.314 | | E(DIHE)=0.000 E(IMPR)=92.379 E(VDW )=-260.689 E(ELEC)=-131.398 | | E(CDIH)=2.166 E(NOE )=66.331 E(PLAN)=15.825 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=19.452 E(kin)=14.228 temperature=7.051 | | Etotal =19.448 grad(E)=1.954 E(BOND)=10.946 E(ANGL)=12.694 | | E(DIHE)=0.000 E(IMPR)=7.586 E(VDW )=6.215 E(ELEC)=7.638 | | E(CDIH)=1.517 E(NOE )=8.355 E(PLAN)=1.966 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61973 intra-atom interactions NBONDS: found 61963 intra-atom interactions NBONDS: found 61930 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61993 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61943 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=922.924 E(kin)=587.317 temperature=291.040 | | Etotal =335.607 grad(E)=70.333 E(BOND)=207.312 E(ANGL)=339.252 | | E(DIHE)=0.000 E(IMPR)=102.599 E(VDW )=-251.876 E(ELEC)=-138.576 | | E(CDIH)=1.803 E(NOE )=62.221 E(PLAN)=12.872 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61879 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61857 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61845 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61825 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61831 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61816 intra-atom interactions NBONDS: found 61888 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=935.352 E(kin)=618.991 temperature=306.736 | | Etotal =316.361 grad(E)=68.895 E(BOND)=205.160 E(ANGL)=339.622 | | E(DIHE)=0.000 E(IMPR)=91.706 E(VDW )=-257.524 E(ELEC)=-134.807 | | E(CDIH)=1.834 E(NOE )=53.831 E(PLAN)=16.539 | ------------------------------------------------------------------------------- NBONDS: found 61962 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61986 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61966 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61905 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61842 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61854 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61867 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61812 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=919.280 E(kin)=591.546 temperature=293.136 | | Etotal =327.734 grad(E)=68.073 E(BOND)=212.602 E(ANGL)=350.505 | | E(DIHE)=0.000 E(IMPR)=76.588 E(VDW )=-261.569 E(ELEC)=-139.656 | | E(CDIH)=0.727 E(NOE )=68.809 E(PLAN)=19.729 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61762 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61768 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61775 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61813 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61884 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61935 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=938.609 E(kin)=587.222 temperature=290.993 | | Etotal =351.386 grad(E)=67.225 E(BOND)=199.784 E(ANGL)=383.552 | | E(DIHE)=0.000 E(IMPR)=85.241 E(VDW )=-250.535 E(ELEC)=-147.996 | | E(CDIH)=2.777 E(NOE )=61.524 E(PLAN)=17.040 | ------------------------------------------------------------------------------- NBONDS: found 61977 intra-atom interactions NBONDS: found 61953 intra-atom interactions NBONDS: found 61910 intra-atom interactions NBONDS: found 61836 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61800 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61807 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61829 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61815 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61874 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61905 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=929.784 E(kin)=628.217 temperature=311.308 | | Etotal =301.568 grad(E)=65.716 E(BOND)=197.725 E(ANGL)=330.412 | | E(DIHE)=0.000 E(IMPR)=86.000 E(VDW )=-259.770 E(ELEC)=-135.526 | | E(CDIH)=2.372 E(NOE )=60.959 E(PLAN)=19.395 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61918 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61980 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62004 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62082 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62108 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62137 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62227 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62301 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62322 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62354 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62404 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=941.986 E(kin)=617.147 temperature=305.822 | | Etotal =324.839 grad(E)=66.788 E(BOND)=203.329 E(ANGL)=344.070 | | E(DIHE)=0.000 E(IMPR)=90.704 E(VDW )=-254.406 E(ELEC)=-138.209 | | E(CDIH)=4.472 E(NOE )=57.806 E(PLAN)=17.074 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62440 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62474 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62506 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62507 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62501 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 62528 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62495 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62506 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62517 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=911.892 E(kin)=616.897 temperature=305.698 | | Etotal =294.996 grad(E)=66.920 E(BOND)=190.236 E(ANGL)=337.518 | | E(DIHE)=0.000 E(IMPR)=84.076 E(VDW )=-255.686 E(ELEC)=-143.009 | | E(CDIH)=1.013 E(NOE )=62.859 E(PLAN)=17.989 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62467 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62525 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62508 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62477 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62449 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62412 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62442 intra-atom interactions NBONDS: found 62401 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=918.955 E(kin)=592.015 temperature=293.369 | | Etotal =326.940 grad(E)=69.839 E(BOND)=210.641 E(ANGL)=356.376 | | E(DIHE)=0.000 E(IMPR)=81.148 E(VDW )=-275.043 E(ELEC)=-135.488 | | E(CDIH)=3.327 E(NOE )=69.734 E(PLAN)=16.244 | ------------------------------------------------------------------------------- NBONDS: found 62318 intra-atom interactions NBONDS: found 62231 intra-atom interactions NBONDS: found 62117 intra-atom interactions NBONDS: found 62003 intra-atom interactions NBONDS: found 61893 intra-atom interactions NBONDS: found 61778 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61725 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61660 intra-atom interactions NBONDS: found 61627 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=923.116 E(kin)=595.841 temperature=295.264 | | Etotal =327.275 grad(E)=71.197 E(BOND)=209.661 E(ANGL)=342.085 | | E(DIHE)=0.000 E(IMPR)=91.494 E(VDW )=-263.620 E(ELEC)=-137.740 | | E(CDIH)=4.996 E(NOE )=65.146 E(PLAN)=15.251 | ------------------------------------------------------------------------------- NBONDS: found 61535 intra-atom interactions NBONDS: found 61443 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61354 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61289 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61229 intra-atom interactions NBONDS: found 61215 intra-atom interactions NBONDS: found 61258 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=920.802 E(kin)=623.623 temperature=309.031 | | Etotal =297.179 grad(E)=69.331 E(BOND)=210.346 E(ANGL)=322.346 | | E(DIHE)=0.000 E(IMPR)=98.510 E(VDW )=-270.224 E(ELEC)=-140.514 | | E(CDIH)=3.353 E(NOE )=55.865 E(PLAN)=17.497 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=929.937 E(kin)=605.553 temperature=300.077 | | Etotal =324.385 grad(E)=67.794 E(BOND)=211.527 E(ANGL)=340.050 | | E(DIHE)=0.000 E(IMPR)=89.592 E(VDW )=-261.490 E(ELEC)=-139.033 | | E(CDIH)=2.086 E(NOE )=65.825 E(PLAN)=15.829 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.657 E(kin)=12.433 temperature=6.161 | | Etotal =15.462 grad(E)=1.809 E(BOND)=9.591 E(ANGL)=11.472 | | E(DIHE)=0.000 E(IMPR)=7.363 E(VDW )=5.386 E(ELEC)=3.676 | | E(CDIH)=1.294 E(NOE )=6.510 E(PLAN)=1.822 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=932.982 E(kin)=605.216 temperature=299.910 | | Etotal =327.766 grad(E)=66.410 E(BOND)=207.847 E(ANGL)=336.781 | | E(DIHE)=0.000 E(IMPR)=92.031 E(VDW )=-260.789 E(ELEC)=-132.352 | | E(CDIH)=2.156 E(NOE )=66.268 E(PLAN)=15.825 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=18.549 E(kin)=14.017 temperature=6.946 | | Etotal =19.039 grad(E)=2.006 E(BOND)=10.875 E(ANGL)=12.609 | | E(DIHE)=0.000 E(IMPR)=7.614 E(VDW )=6.124 E(ELEC)=7.688 | | E(CDIH)=1.491 E(NOE )=8.149 E(PLAN)=1.948 | ------------------------------------------------------------------------------- NBONDS: found 61325 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61359 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61342 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 61360 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 61420 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 61453 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61461 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61442 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=938.917 E(kin)=615.029 temperature=304.773 | | Etotal =323.888 grad(E)=65.582 E(BOND)=204.884 E(ANGL)=347.745 | | E(DIHE)=0.000 E(IMPR)=79.655 E(VDW )=-264.066 E(ELEC)=-137.061 | | E(CDIH)=0.668 E(NOE )=77.056 E(PLAN)=15.006 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61511 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61639 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61631 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61725 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61746 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61782 intra-atom interactions NBONDS: found 61817 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=900.476 E(kin)=586.258 temperature=290.516 | | Etotal =314.218 grad(E)=66.986 E(BOND)=194.452 E(ANGL)=345.213 | | E(DIHE)=0.000 E(IMPR)=93.504 E(VDW )=-262.002 E(ELEC)=-135.884 | | E(CDIH)=1.960 E(NOE )=60.028 E(PLAN)=16.947 | ------------------------------------------------------------------------------- NBONDS: found 61828 intra-atom interactions NBONDS: found 61853 intra-atom interactions NBONDS: found 61910 intra-atom interactions NBONDS: found 62000 intra-atom interactions NBONDS: found 62093 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62182 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62233 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62285 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=921.034 E(kin)=622.004 temperature=308.229 | | Etotal =299.031 grad(E)=67.905 E(BOND)=193.626 E(ANGL)=326.585 | | E(DIHE)=0.000 E(IMPR)=91.828 E(VDW )=-253.971 E(ELEC)=-141.999 | | E(CDIH)=0.871 E(NOE )=63.015 E(PLAN)=19.075 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62366 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62352 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62318 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62312 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62254 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62177 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62136 intra-atom interactions NBONDS: found 62116 intra-atom interactions NBONDS: found 62036 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62036 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=930.521 E(kin)=599.698 temperature=297.175 | | Etotal =330.823 grad(E)=68.959 E(BOND)=195.644 E(ANGL)=357.183 | | E(DIHE)=0.000 E(IMPR)=95.001 E(VDW )=-267.866 E(ELEC)=-129.075 | | E(CDIH)=1.092 E(NOE )=63.951 E(PLAN)=14.895 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61982 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61947 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61878 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61885 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61871 intra-atom interactions NBONDS: found 61856 intra-atom interactions NBONDS: found 61896 intra-atom interactions NBONDS: found 61856 intra-atom interactions NBONDS: found 61816 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=927.805 E(kin)=599.251 temperature=296.954 | | Etotal =328.555 grad(E)=67.640 E(BOND)=234.299 E(ANGL)=345.670 | | E(DIHE)=0.000 E(IMPR)=82.360 E(VDW )=-257.853 E(ELEC)=-142.508 | | E(CDIH)=0.609 E(NOE )=51.683 E(PLAN)=14.295 | ------------------------------------------------------------------------------- NBONDS: found 61824 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61820 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61753 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61779 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61765 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61749 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H4' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61687 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61692 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61678 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=934.923 E(kin)=596.846 temperature=295.762 | | Etotal =338.076 grad(E)=71.681 E(BOND)=232.584 E(ANGL)=330.141 | | E(DIHE)=0.000 E(IMPR)=89.474 E(VDW )=-264.022 E(ELEC)=-137.158 | | E(CDIH)=2.591 E(NOE )=67.552 E(PLAN)=16.913 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61703 intra-atom interactions NBONDS: found 61719 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61771 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61835 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61845 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61869 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61893 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=944.503 E(kin)=612.024 temperature=303.284 | | Etotal =332.478 grad(E)=69.786 E(BOND)=224.665 E(ANGL)=336.894 | | E(DIHE)=0.000 E(IMPR)=91.823 E(VDW )=-263.392 E(ELEC)=-138.998 | | E(CDIH)=2.335 E(NOE )=60.629 E(PLAN)=18.523 | ------------------------------------------------------------------------------- NBONDS: found 61878 intra-atom interactions NBONDS: found 61964 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.43 A apart NBONDS: found 62008 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart NBONDS: found 62011 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61986 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61908 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=928.226 E(kin)=616.506 temperature=305.505 | | Etotal =311.720 grad(E)=66.881 E(BOND)=209.487 E(ANGL)=337.884 | | E(DIHE)=0.000 E(IMPR)=87.064 E(VDW )=-259.765 E(ELEC)=-132.261 | | E(CDIH)=1.698 E(NOE )=56.523 E(PLAN)=11.090 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61859 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61740 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61687 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61643 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61625 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61628 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61706 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=940.950 E(kin)=621.533 temperature=307.996 | | Etotal =319.417 grad(E)=67.321 E(BOND)=226.099 E(ANGL)=333.064 | | E(DIHE)=0.000 E(IMPR)=88.223 E(VDW )=-264.253 E(ELEC)=-139.794 | | E(CDIH)=2.139 E(NOE )=60.736 E(PLAN)=13.202 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61820 intra-atom interactions NBONDS: found 61931 intra-atom interactions NBONDS: found 62072 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62134 intra-atom interactions NBONDS: found 62173 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.47 A apart NBONDS: found 62207 intra-atom interactions NBONDS: found 62092 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=932.193 E(kin)=612.161 temperature=303.351 | | Etotal =320.032 grad(E)=68.037 E(BOND)=206.964 E(ANGL)=335.551 | | E(DIHE)=0.000 E(IMPR)=92.660 E(VDW )=-253.377 E(ELEC)=-142.878 | | E(CDIH)=2.736 E(NOE )=61.230 E(PLAN)=17.146 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.800 E(kin)=605.437 temperature=300.019 | | Etotal =325.363 grad(E)=68.063 E(BOND)=214.286 E(ANGL)=338.947 | | E(DIHE)=0.000 E(IMPR)=91.031 E(VDW )=-260.525 E(ELEC)=-138.308 | | E(CDIH)=1.930 E(NOE )=62.215 E(PLAN)=15.787 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.673 E(kin)=12.636 temperature=6.262 | | Etotal =16.215 grad(E)=1.781 E(BOND)=9.983 E(ANGL)=11.813 | | E(DIHE)=0.000 E(IMPR)=7.016 E(VDW )=4.800 E(ELEC)=4.240 | | E(CDIH)=1.293 E(NOE )=6.684 E(PLAN)=2.195 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=932.740 E(kin)=605.240 temperature=299.922 | | Etotal =327.499 grad(E)=66.594 E(BOND)=208.562 E(ANGL)=337.021 | | E(DIHE)=0.000 E(IMPR)=91.920 E(VDW )=-260.759 E(ELEC)=-133.014 | | E(CDIH)=2.131 E(NOE )=65.818 E(PLAN)=15.821 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=17.859 E(kin)=13.871 temperature=6.874 | | Etotal =18.761 grad(E)=2.049 E(BOND)=10.968 E(ANGL)=12.541 | | E(DIHE)=0.000 E(IMPR)=7.557 E(VDW )=5.992 E(ELEC)=7.618 | | E(CDIH)=1.472 E(NOE )=8.100 E(PLAN)=1.977 | ------------------------------------------------------------------------------- NBONDS: found 62085 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.44 A apart NBONDS: found 62035 intra-atom interactions NBONDS: found 61991 intra-atom interactions NBONDS: found 61899 intra-atom interactions NBONDS: found 61824 intra-atom interactions NBONDS: found 61769 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61731 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61716 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61653 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=931.646 E(kin)=600.929 temperature=297.786 | | Etotal =330.717 grad(E)=67.452 E(BOND)=231.876 E(ANGL)=340.586 | | E(DIHE)=0.000 E(IMPR)=85.993 E(VDW )=-249.954 E(ELEC)=-142.420 | | E(CDIH)=2.104 E(NOE )=47.125 E(PLAN)=15.408 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61578 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61498 intra-atom interactions NBONDS: found 61502 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61479 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61484 intra-atom interactions NBONDS: found 61502 intra-atom interactions NBONDS: found 61561 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.46 A apart NBONDS: found 61563 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=943.777 E(kin)=602.321 temperature=298.475 | | Etotal =341.457 grad(E)=71.949 E(BOND)=214.482 E(ANGL)=331.408 | | E(DIHE)=0.000 E(IMPR)=108.883 E(VDW )=-253.831 E(ELEC)=-145.823 | | E(CDIH)=0.251 E(NOE )=71.358 E(PLAN)=14.729 | ------------------------------------------------------------------------------- NBONDS: found 61602 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61571 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61553 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61510 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61557 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=931.859 E(kin)=595.522 temperature=295.106 | | Etotal =336.337 grad(E)=68.928 E(BOND)=207.559 E(ANGL)=341.174 | | E(DIHE)=0.000 E(IMPR)=109.587 E(VDW )=-263.518 E(ELEC)=-138.009 | | E(CDIH)=2.388 E(NOE )=60.342 E(PLAN)=16.814 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61544 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61477 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61435 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 61449 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.33 A apart NBONDS: found 61430 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 61272 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 61301 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61307 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=920.871 E(kin)=611.572 temperature=303.059 | | Etotal =309.300 grad(E)=69.128 E(BOND)=206.866 E(ANGL)=328.842 | | E(DIHE)=0.000 E(IMPR)=97.348 E(VDW )=-265.838 E(ELEC)=-143.502 | | E(CDIH)=1.857 E(NOE )=66.212 E(PLAN)=17.515 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61298 intra-atom interactions NBONDS: found 61346 intra-atom interactions NBONDS: found 61404 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61444 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61469 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61440 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61443 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61477 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=941.012 E(kin)=604.639 temperature=299.624 | | Etotal =336.373 grad(E)=70.951 E(BOND)=213.373 E(ANGL)=347.336 | | E(DIHE)=0.000 E(IMPR)=101.142 E(VDW )=-262.685 E(ELEC)=-143.724 | | E(CDIH)=4.309 E(NOE )=59.504 E(PLAN)=17.118 | ------------------------------------------------------------------------------- NBONDS: found 61537 intra-atom interactions NBONDS: found 61643 intra-atom interactions NBONDS: found 61706 intra-atom interactions NBONDS: found 61754 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61755 intra-atom interactions NBONDS: found 61829 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61847 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=929.584 E(kin)=604.434 temperature=299.523 | | Etotal =325.150 grad(E)=68.659 E(BOND)=212.834 E(ANGL)=348.813 | | E(DIHE)=0.000 E(IMPR)=89.491 E(VDW )=-260.535 E(ELEC)=-142.969 | | E(CDIH)=1.766 E(NOE )=58.589 E(PLAN)=17.161 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61911 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61971 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61947 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62001 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62027 intra-atom interactions NBONDS: found 62125 intra-atom interactions NBONDS: found 62193 intra-atom interactions NBONDS: found 62224 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=942.272 E(kin)=611.092 temperature=302.822 | | Etotal =331.179 grad(E)=68.572 E(BOND)=205.661 E(ANGL)=348.400 | | E(DIHE)=0.000 E(IMPR)=101.981 E(VDW )=-273.212 E(ELEC)=-127.269 | | E(CDIH)=0.899 E(NOE )=58.515 E(PLAN)=16.204 | ------------------------------------------------------------------------------- NBONDS: found 62301 intra-atom interactions NBONDS: found 62371 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62446 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62458 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62426 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62428 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62439 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62387 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=925.758 E(kin)=603.790 temperature=299.203 | | Etotal =321.968 grad(E)=69.889 E(BOND)=216.621 E(ANGL)=339.249 | | E(DIHE)=0.000 E(IMPR)=96.510 E(VDW )=-261.323 E(ELEC)=-135.698 | | E(CDIH)=0.573 E(NOE )=50.628 E(PLAN)=15.408 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62334 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62293 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62280 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62227 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62273 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62270 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62256 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62313 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62318 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=941.269 E(kin)=606.090 temperature=300.343 | | Etotal =335.179 grad(E)=72.936 E(BOND)=210.376 E(ANGL)=352.058 | | E(DIHE)=0.000 E(IMPR)=90.676 E(VDW )=-261.050 E(ELEC)=-136.666 | | E(CDIH)=1.486 E(NOE )=61.838 E(PLAN)=16.460 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62364 intra-atom interactions NBONDS: found 62404 intra-atom interactions NBONDS: found 62457 intra-atom interactions NBONDS: found 62467 intra-atom interactions NBONDS: found 62470 intra-atom interactions NBONDS: found 62464 intra-atom interactions NBONDS: found 62481 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62451 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=933.591 E(kin)=617.982 temperature=306.236 | | Etotal =315.610 grad(E)=68.104 E(BOND)=216.673 E(ANGL)=337.845 | | E(DIHE)=0.000 E(IMPR)=87.144 E(VDW )=-268.851 E(ELEC)=-140.363 | | E(CDIH)=2.013 E(NOE )=64.031 E(PLAN)=17.117 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=932.665 E(kin)=605.496 temperature=300.049 | | Etotal =327.169 grad(E)=69.299 E(BOND)=212.983 E(ANGL)=339.622 | | E(DIHE)=0.000 E(IMPR)=95.903 E(VDW )=-260.236 E(ELEC)=-139.925 | | E(CDIH)=1.969 E(NOE )=60.826 E(PLAN)=16.027 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.348 E(kin)=12.715 temperature=6.301 | | Etotal =14.903 grad(E)=1.790 E(BOND)=9.364 E(ANGL)=12.269 | | E(DIHE)=0.000 E(IMPR)=6.928 E(VDW )=4.728 E(ELEC)=5.311 | | E(CDIH)=1.385 E(NOE )=6.293 E(PLAN)=1.994 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=932.732 E(kin)=605.266 temperature=299.935 | | Etotal =327.466 grad(E)=66.864 E(BOND)=209.004 E(ANGL)=337.281 | | E(DIHE)=0.000 E(IMPR)=92.318 E(VDW )=-260.707 E(ELEC)=-133.705 | | E(CDIH)=2.115 E(NOE )=65.319 E(PLAN)=15.842 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=17.147 E(kin)=13.760 temperature=6.819 | | Etotal =18.412 grad(E)=2.181 E(BOND)=10.899 E(ANGL)=12.539 | | E(DIHE)=0.000 E(IMPR)=7.591 E(VDW )=5.880 E(ELEC)=7.704 | | E(CDIH)=1.464 E(NOE )=8.078 E(PLAN)=1.980 | ------------------------------------------------------------------------------- NBONDS: found 62479 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62519 intra-atom interactions NBONDS: found 62481 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62457 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62453 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62386 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62346 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62320 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=942.285 E(kin)=608.407 temperature=301.491 | | Etotal =333.878 grad(E)=69.660 E(BOND)=190.843 E(ANGL)=347.496 | | E(DIHE)=0.000 E(IMPR)=95.869 E(VDW )=-254.642 E(ELEC)=-131.143 | | E(CDIH)=1.658 E(NOE )=70.639 E(PLAN)=13.159 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62289 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62269 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62226 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62211 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62129 intra-atom interactions NBONDS: found 62085 intra-atom interactions NBONDS: found 62050 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=927.415 E(kin)=613.149 temperature=303.841 | | Etotal =314.266 grad(E)=68.551 E(BOND)=199.629 E(ANGL)=341.987 | | E(DIHE)=0.000 E(IMPR)=93.987 E(VDW )=-269.708 E(ELEC)=-132.269 | | E(CDIH)=0.676 E(NOE )=60.542 E(PLAN)=19.422 | ------------------------------------------------------------------------------- NBONDS: found 62063 intra-atom interactions NBONDS: found 61973 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61927 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61892 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61882 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61933 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61969 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=930.345 E(kin)=598.922 temperature=296.791 | | Etotal =331.423 grad(E)=67.577 E(BOND)=218.603 E(ANGL)=339.503 | | E(DIHE)=0.000 E(IMPR)=90.803 E(VDW )=-254.105 E(ELEC)=-140.622 | | E(CDIH)=1.911 E(NOE )=58.674 E(PLAN)=16.656 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61958 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61991 intra-atom interactions NBONDS: found 62061 intra-atom interactions NBONDS: found 62020 intra-atom interactions NBONDS: found 62003 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61945 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61988 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62017 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62044 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62055 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62097 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=945.406 E(kin)=610.547 temperature=302.552 | | Etotal =334.859 grad(E)=69.979 E(BOND)=227.265 E(ANGL)=334.616 | | E(DIHE)=0.000 E(IMPR)=94.025 E(VDW )=-253.330 E(ELEC)=-134.164 | | E(CDIH)=1.094 E(NOE )=50.704 E(PLAN)=14.648 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62115 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62134 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62149 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62122 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62156 intra-atom interactions NBONDS: found 62192 intra-atom interactions NBONDS: found 62166 intra-atom interactions NBONDS: found 62160 intra-atom interactions NBONDS: found 62160 intra-atom interactions NBONDS: found 62188 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=932.874 E(kin)=610.229 temperature=302.394 | | Etotal =322.645 grad(E)=67.980 E(BOND)=208.770 E(ANGL)=340.892 | | E(DIHE)=0.000 E(IMPR)=92.354 E(VDW )=-260.758 E(ELEC)=-132.996 | | E(CDIH)=1.911 E(NOE )=57.798 E(PLAN)=14.674 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62160 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62149 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62144 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62118 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62054 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61988 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62026 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61997 intra-atom interactions NBONDS: found 62014 intra-atom interactions NBONDS: found 62026 intra-atom interactions NBONDS: found 62018 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=945.731 E(kin)=611.689 temperature=303.118 | | Etotal =334.042 grad(E)=70.340 E(BOND)=215.633 E(ANGL)=332.414 | | E(DIHE)=0.000 E(IMPR)=101.969 E(VDW )=-267.944 E(ELEC)=-129.628 | | E(CDIH)=1.763 E(NOE )=64.727 E(PLAN)=15.108 | ------------------------------------------------------------------------------- NBONDS: found 61997 intra-atom interactions NBONDS: found 61957 intra-atom interactions NBONDS: found 61902 intra-atom interactions NBONDS: found 61904 intra-atom interactions NBONDS: found 61939 intra-atom interactions NBONDS: found 61924 intra-atom interactions NBONDS: found 61931 intra-atom interactions NBONDS: found 61880 intra-atom interactions NBONDS: found 61885 intra-atom interactions NBONDS: found 61903 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=946.450 E(kin)=601.057 temperature=297.849 | | Etotal =345.394 grad(E)=68.271 E(BOND)=221.481 E(ANGL)=350.397 | | E(DIHE)=0.000 E(IMPR)=93.120 E(VDW )=-264.314 E(ELEC)=-127.907 | | E(CDIH)=4.080 E(NOE )=52.649 E(PLAN)=15.888 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61994 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62059 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62067 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62126 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62152 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62121 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62185 intra-atom interactions NBONDS: found 62154 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=935.137 E(kin)=598.764 temperature=296.713 | | Etotal =336.373 grad(E)=69.582 E(BOND)=228.807 E(ANGL)=337.118 | | E(DIHE)=0.000 E(IMPR)=89.689 E(VDW )=-257.339 E(ELEC)=-140.899 | | E(CDIH)=0.859 E(NOE )=62.185 E(PLAN)=15.952 | ------------------------------------------------------------------------------- NBONDS: found 62166 intra-atom interactions NBONDS: found 62138 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62097 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62176 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62163 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62122 intra-atom interactions NBONDS: found 62101 intra-atom interactions NBONDS: found 62075 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=928.386 E(kin)=607.451 temperature=301.017 | | Etotal =320.935 grad(E)=70.248 E(BOND)=219.665 E(ANGL)=327.959 | | E(DIHE)=0.000 E(IMPR)=90.406 E(VDW )=-266.862 E(ELEC)=-134.761 | | E(CDIH)=1.380 E(NOE )=71.968 E(PLAN)=11.181 | ------------------------------------------------------------------------------- NBONDS: found 62043 intra-atom interactions NBONDS: found 62025 intra-atom interactions NBONDS: found 62036 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61992 intra-atom interactions NBONDS: found 61991 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62040 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62077 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62144 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62152 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62223 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=917.775 E(kin)=621.101 temperature=307.782 | | Etotal =296.673 grad(E)=68.367 E(BOND)=191.510 E(ANGL)=342.376 | | E(DIHE)=0.000 E(IMPR)=99.570 E(VDW )=-264.253 E(ELEC)=-139.251 | | E(CDIH)=1.417 E(NOE )=47.583 E(PLAN)=17.721 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=935.667 E(kin)=605.566 temperature=300.083 | | Etotal =330.101 grad(E)=69.496 E(BOND)=213.750 E(ANGL)=339.218 | | E(DIHE)=0.000 E(IMPR)=94.844 E(VDW )=-261.435 E(ELEC)=-134.107 | | E(CDIH)=1.988 E(NOE )=59.916 E(PLAN)=15.928 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.790 E(kin)=13.070 temperature=6.477 | | Etotal =16.675 grad(E)=1.787 E(BOND)=10.149 E(ANGL)=11.600 | | E(DIHE)=0.000 E(IMPR)=7.233 E(VDW )=5.222 E(ELEC)=4.555 | | E(CDIH)=1.355 E(NOE )=5.766 E(PLAN)=1.588 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=932.999 E(kin)=605.293 temperature=299.948 | | Etotal =327.706 grad(E)=67.104 E(BOND)=209.436 E(ANGL)=337.457 | | E(DIHE)=0.000 E(IMPR)=92.548 E(VDW )=-260.773 E(ELEC)=-133.742 | | E(CDIH)=2.103 E(NOE )=64.828 E(PLAN)=15.849 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=16.691 E(kin)=13.699 temperature=6.788 | | Etotal =18.277 grad(E)=2.278 E(BOND)=10.919 E(ANGL)=12.469 | | E(DIHE)=0.000 E(IMPR)=7.594 E(VDW )=5.827 E(ELEC)=7.474 | | E(CDIH)=1.455 E(NOE )=8.047 E(PLAN)=1.948 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62290 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62301 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62332 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62317 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62294 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62203 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62113 intra-atom interactions NBONDS: found 62069 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=936.507 E(kin)=625.794 temperature=310.107 | | Etotal =310.713 grad(E)=68.871 E(BOND)=196.738 E(ANGL)=339.306 | | E(DIHE)=0.000 E(IMPR)=101.457 E(VDW )=-267.929 E(ELEC)=-140.979 | | E(CDIH)=1.458 E(NOE )=66.281 E(PLAN)=14.379 | ------------------------------------------------------------------------------- NBONDS: found 62015 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61972 intra-atom interactions NBONDS: found 61998 intra-atom interactions NBONDS: found 61992 intra-atom interactions NBONDS: found 62018 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62067 intra-atom interactions NBONDS: found 62014 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62119 intra-atom interactions NBONDS: found 62168 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62172 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=923.647 E(kin)=622.339 temperature=308.395 | | Etotal =301.307 grad(E)=69.785 E(BOND)=207.887 E(ANGL)=318.301 | | E(DIHE)=0.000 E(IMPR)=94.599 E(VDW )=-253.660 E(ELEC)=-136.878 | | E(CDIH)=2.310 E(NOE )=53.101 E(PLAN)=15.648 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62202 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62261 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62267 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62303 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62249 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62285 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62278 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62273 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62254 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62247 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=935.659 E(kin)=606.818 temperature=300.704 | | Etotal =328.841 grad(E)=67.727 E(BOND)=224.640 E(ANGL)=340.340 | | E(DIHE)=0.000 E(IMPR)=81.411 E(VDW )=-262.831 E(ELEC)=-131.793 | | E(CDIH)=4.925 E(NOE )=58.912 E(PLAN)=13.237 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62261 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62322 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62344 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62412 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62567 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62609 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62632 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=927.760 E(kin)=612.425 temperature=303.483 | | Etotal =315.335 grad(E)=68.621 E(BOND)=207.619 E(ANGL)=339.988 | | E(DIHE)=0.000 E(IMPR)=90.820 E(VDW )=-261.703 E(ELEC)=-135.315 | | E(CDIH)=0.490 E(NOE )=58.482 E(PLAN)=14.954 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62621 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62607 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62606 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62611 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62590 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62583 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62536 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62550 intra-atom interactions NBONDS: found 62430 intra-atom interactions NBONDS: found 62394 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=948.359 E(kin)=586.879 temperature=290.823 | | Etotal =361.480 grad(E)=70.742 E(BOND)=214.851 E(ANGL)=360.163 | | E(DIHE)=0.000 E(IMPR)=104.449 E(VDW )=-251.836 E(ELEC)=-138.336 | | E(CDIH)=0.454 E(NOE )=55.883 E(PLAN)=15.850 | ------------------------------------------------------------------------------- NBONDS: found 62236 intra-atom interactions NBONDS: found 62193 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62131 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62096 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62065 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62104 intra-atom interactions NBONDS: found 62159 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=947.443 E(kin)=622.500 temperature=308.475 | | Etotal =324.943 grad(E)=70.527 E(BOND)=214.773 E(ANGL)=339.737 | | E(DIHE)=0.000 E(IMPR)=102.134 E(VDW )=-265.235 E(ELEC)=-139.861 | | E(CDIH)=1.837 E(NOE )=56.487 E(PLAN)=15.071 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62229 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62305 intra-atom interactions NBONDS: found 62345 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62428 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62407 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62431 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62416 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62413 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62418 intra-atom interactions NBONDS: found 62423 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=938.996 E(kin)=596.925 temperature=295.801 | | Etotal =342.072 grad(E)=70.075 E(BOND)=224.177 E(ANGL)=364.931 | | E(DIHE)=0.000 E(IMPR)=79.693 E(VDW )=-263.134 E(ELEC)=-138.624 | | E(CDIH)=1.353 E(NOE )=55.971 E(PLAN)=17.706 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62404 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62361 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62323 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62328 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62294 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62282 intra-atom interactions %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62309 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62270 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=923.686 E(kin)=602.497 temperature=298.562 | | Etotal =321.189 grad(E)=73.596 E(BOND)=205.128 E(ANGL)=332.317 | | E(DIHE)=0.000 E(IMPR)=106.632 E(VDW )=-265.120 E(ELEC)=-144.480 | | E(CDIH)=2.460 E(NOE )=71.330 E(PLAN)=12.923 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62210 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 62151 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62145 intra-atom interactions NBONDS: found 62088 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61948 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61924 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 61900 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61819 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=938.170 E(kin)=613.631 temperature=304.080 | | Etotal =324.539 grad(E)=70.187 E(BOND)=203.981 E(ANGL)=343.626 | | E(DIHE)=0.000 E(IMPR)=105.053 E(VDW )=-259.641 E(ELEC)=-146.150 | | E(CDIH)=2.929 E(NOE )=57.832 E(PLAN)=16.909 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61710 intra-atom interactions NBONDS: found 61664 intra-atom interactions NBONDS: found 61613 intra-atom interactions NBONDS: found 61660 intra-atom interactions NBONDS: found 61736 intra-atom interactions NBONDS: found 61804 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=930.109 E(kin)=627.283 temperature=310.845 | | Etotal =302.827 grad(E)=69.941 E(BOND)=208.334 E(ANGL)=335.312 | | E(DIHE)=0.000 E(IMPR)=91.807 E(VDW )=-257.618 E(ELEC)=-149.101 | | E(CDIH)=2.283 E(NOE )=55.046 E(PLAN)=16.764 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=934.618 E(kin)=605.465 temperature=300.034 | | Etotal =329.152 grad(E)=70.033 E(BOND)=217.292 E(ANGL)=336.170 | | E(DIHE)=0.000 E(IMPR)=98.876 E(VDW )=-262.434 E(ELEC)=-137.949 | | E(CDIH)=2.020 E(NOE )=59.432 E(PLAN)=15.746 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.263 E(kin)=12.817 temperature=6.351 | | Etotal =16.140 grad(E)=1.946 E(BOND)=9.828 E(ANGL)=10.747 | | E(DIHE)=0.000 E(IMPR)=7.703 E(VDW )=4.573 E(ELEC)=5.240 | | E(CDIH)=1.365 E(NOE )=5.598 E(PLAN)=1.898 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=933.134 E(kin)=605.308 temperature=299.955 | | Etotal =327.826 grad(E)=67.348 E(BOND)=210.090 E(ANGL)=337.350 | | E(DIHE)=0.000 E(IMPR)=93.075 E(VDW )=-260.912 E(ELEC)=-134.092 | | E(CDIH)=2.096 E(NOE )=64.378 E(PLAN)=15.841 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=16.259 E(kin)=13.628 temperature=6.753 | | Etotal =18.113 grad(E)=2.393 E(BOND)=11.047 E(ANGL)=12.339 | | E(DIHE)=0.000 E(IMPR)=7.802 E(VDW )=5.751 E(ELEC)=7.406 | | E(CDIH)=1.448 E(NOE )=8.012 E(PLAN)=1.944 | ------------------------------------------------------------------------------- NBONDS: found 61829 intra-atom interactions NBONDS: found 61816 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61840 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61823 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 61796 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61755 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61755 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61736 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=934.123 E(kin)=637.712 temperature=316.013 | | Etotal =296.411 grad(E)=67.239 E(BOND)=197.113 E(ANGL)=325.402 | | E(DIHE)=0.000 E(IMPR)=95.707 E(VDW )=-256.982 E(ELEC)=-141.074 | | E(CDIH)=2.196 E(NOE )=59.059 E(PLAN)=14.991 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61747 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61750 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61793 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61837 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61856 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61895 intra-atom interactions NBONDS: found 61917 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=931.800 E(kin)=594.065 temperature=294.384 | | Etotal =337.735 grad(E)=72.659 E(BOND)=207.421 E(ANGL)=343.249 | | E(DIHE)=0.000 E(IMPR)=108.604 E(VDW )=-260.953 E(ELEC)=-133.495 | | E(CDIH)=1.492 E(NOE )=55.771 E(PLAN)=15.646 | ------------------------------------------------------------------------------- NBONDS: found 61973 intra-atom interactions NBONDS: found 61976 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62020 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61997 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61915 intra-atom interactions NBONDS: found 61878 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=922.737 E(kin)=611.858 temperature=303.201 | | Etotal =310.879 grad(E)=69.981 E(BOND)=192.212 E(ANGL)=351.308 | | E(DIHE)=0.000 E(IMPR)=106.649 E(VDW )=-264.542 E(ELEC)=-150.609 | | E(CDIH)=2.254 E(NOE )=58.265 E(PLAN)=15.342 | ------------------------------------------------------------------------------- NBONDS: found 61882 intra-atom interactions NBONDS: found 61862 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61837 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61814 intra-atom interactions NBONDS: found 61797 intra-atom interactions NBONDS: found 61782 intra-atom interactions NBONDS: found 61769 intra-atom interactions NBONDS: found 61779 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61763 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61768 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=935.633 E(kin)=605.979 temperature=300.288 | | Etotal =329.654 grad(E)=69.188 E(BOND)=196.913 E(ANGL)=380.175 | | E(DIHE)=0.000 E(IMPR)=90.860 E(VDW )=-263.883 E(ELEC)=-144.813 | | E(CDIH)=1.027 E(NOE )=52.069 E(PLAN)=17.305 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61795 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61798 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61771 intra-atom interactions NBONDS: found 61833 intra-atom interactions NBONDS: found 61802 intra-atom interactions NBONDS: found 61839 intra-atom interactions NBONDS: found 61812 intra-atom interactions NBONDS: found 61724 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=928.259 E(kin)=607.120 temperature=300.854 | | Etotal =321.139 grad(E)=67.991 E(BOND)=222.522 E(ANGL)=333.633 | | E(DIHE)=0.000 E(IMPR)=90.210 E(VDW )=-273.973 E(ELEC)=-137.254 | | E(CDIH)=4.270 E(NOE )=65.065 E(PLAN)=16.665 | ------------------------------------------------------------------------------- NBONDS: found 61746 intra-atom interactions NBONDS: found 61672 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61663 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61629 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61628 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61628 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61697 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61685 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.49 A apart NBONDS: found 61706 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=925.117 E(kin)=614.525 temperature=304.523 | | Etotal =310.592 grad(E)=68.041 E(BOND)=216.340 E(ANGL)=333.450 | | E(DIHE)=0.000 E(IMPR)=82.327 E(VDW )=-261.092 E(ELEC)=-134.586 | | E(CDIH)=1.492 E(NOE )=56.870 E(PLAN)=15.792 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H5' " only 1.45 A apart NBONDS: found 61716 intra-atom interactions NBONDS: found 61719 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61768 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61778 intra-atom interactions NBONDS: found 61743 intra-atom interactions NBONDS: found 61777 intra-atom interactions NBONDS: found 61760 intra-atom interactions NBONDS: found 61770 intra-atom interactions NBONDS: found 61766 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61821 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=955.576 E(kin)=615.995 temperature=305.251 | | Etotal =339.581 grad(E)=73.147 E(BOND)=211.772 E(ANGL)=343.849 | | E(DIHE)=0.000 E(IMPR)=103.688 E(VDW )=-261.249 E(ELEC)=-145.541 | | E(CDIH)=1.288 E(NOE )=69.764 E(PLAN)=16.011 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61852 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61847 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61912 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61944 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61981 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61975 intra-atom interactions NBONDS: found 62026 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62100 intra-atom interactions NBONDS: found 62066 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=924.566 E(kin)=613.865 temperature=304.196 | | Etotal =310.702 grad(E)=67.322 E(BOND)=218.600 E(ANGL)=320.860 | | E(DIHE)=0.000 E(IMPR)=98.605 E(VDW )=-264.455 E(ELEC)=-136.007 | | E(CDIH)=0.621 E(NOE )=58.084 E(PLAN)=14.393 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62109 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62138 intra-atom interactions NBONDS: found 62150 intra-atom interactions NBONDS: found 62110 intra-atom interactions NBONDS: found 62105 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62122 intra-atom interactions NBONDS: found 62133 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62095 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62124 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62245 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=954.385 E(kin)=608.966 temperature=301.768 | | Etotal =345.420 grad(E)=72.181 E(BOND)=212.795 E(ANGL)=340.515 | | E(DIHE)=0.000 E(IMPR)=104.133 E(VDW )=-256.696 E(ELEC)=-136.645 | | E(CDIH)=0.987 E(NOE )=66.342 E(PLAN)=13.988 | ------------------------------------------------------------------------------- NBONDS: found 62221 intra-atom interactions NBONDS: found 62243 intra-atom interactions NBONDS: found 62282 intra-atom interactions NBONDS: found 62327 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart NBONDS: found 62364 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62471 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62545 intra-atom interactions NBONDS: found 62624 intra-atom interactions NBONDS: found 62735 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=939.811 E(kin)=619.165 temperature=306.822 | | Etotal =320.646 grad(E)=67.033 E(BOND)=218.814 E(ANGL)=335.535 | | E(DIHE)=0.000 E(IMPR)=87.422 E(VDW )=-254.934 E(ELEC)=-136.371 | | E(CDIH)=0.547 E(NOE )=53.567 E(PLAN)=16.066 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=931.447 E(kin)=605.478 temperature=300.040 | | Etotal =325.968 grad(E)=69.980 E(BOND)=215.978 E(ANGL)=338.602 | | E(DIHE)=0.000 E(IMPR)=96.967 E(VDW )=-263.693 E(ELEC)=-140.772 | | E(CDIH)=1.988 E(NOE )=61.282 E(PLAN)=15.616 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.509 E(kin)=13.312 temperature=6.597 | | Etotal =16.117 grad(E)=1.925 E(BOND)=10.053 E(ANGL)=11.811 | | E(DIHE)=0.000 E(IMPR)=7.685 E(VDW )=5.815 E(ELEC)=6.219 | | E(CDIH)=1.265 E(NOE )=6.257 E(PLAN)=1.751 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=933.004 E(kin)=605.321 temperature=299.962 | | Etotal =327.683 grad(E)=67.550 E(BOND)=210.543 E(ANGL)=337.446 | | E(DIHE)=0.000 E(IMPR)=93.374 E(VDW )=-261.126 E(ELEC)=-134.606 | | E(CDIH)=2.088 E(NOE )=64.140 E(PLAN)=15.823 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=15.849 E(kin)=13.604 temperature=6.741 | | Etotal =17.974 grad(E)=2.463 E(BOND)=11.086 E(ANGL)=12.304 | | E(DIHE)=0.000 E(IMPR)=7.861 E(VDW )=5.803 E(ELEC)=7.535 | | E(CDIH)=1.435 E(NOE )=7.934 E(PLAN)=1.931 | ------------------------------------------------------------------------------- NBONDS: found 62752 intra-atom interactions NBONDS: found 62811 intra-atom interactions NBONDS: found 62816 intra-atom interactions NBONDS: found 62795 intra-atom interactions NBONDS: found 62784 intra-atom interactions NBONDS: found 62720 intra-atom interactions NBONDS: found 62675 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62581 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=935.597 E(kin)=596.199 temperature=295.442 | | Etotal =339.398 grad(E)=69.323 E(BOND)=214.646 E(ANGL)=334.341 | | E(DIHE)=0.000 E(IMPR)=101.739 E(VDW )=-246.436 E(ELEC)=-141.400 | | E(CDIH)=2.539 E(NOE )=59.935 E(PLAN)=14.034 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62521 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62380 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62239 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62155 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62063 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62041 intra-atom interactions NBONDS: found 61988 intra-atom interactions NBONDS: found 62059 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=925.678 E(kin)=593.114 temperature=293.913 | | Etotal =332.564 grad(E)=69.241 E(BOND)=225.016 E(ANGL)=341.244 | | E(DIHE)=0.000 E(IMPR)=99.873 E(VDW )=-261.801 E(ELEC)=-139.811 | | E(CDIH)=3.796 E(NOE )=49.358 E(PLAN)=14.889 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62049 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62006 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62046 intra-atom interactions NBONDS: found 62087 intra-atom interactions NBONDS: found 62161 intra-atom interactions NBONDS: found 62140 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart NBONDS: found 62111 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62038 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=928.836 E(kin)=586.732 temperature=290.750 | | Etotal =342.104 grad(E)=69.656 E(BOND)=219.071 E(ANGL)=344.217 | | E(DIHE)=0.000 E(IMPR)=106.564 E(VDW )=-264.884 E(ELEC)=-141.036 | | E(CDIH)=2.420 E(NOE )=63.022 E(PLAN)=12.731 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61989 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61884 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61723 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61662 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61597 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61462 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=933.848 E(kin)=592.419 temperature=293.568 | | Etotal =341.429 grad(E)=69.242 E(BOND)=221.261 E(ANGL)=333.750 | | E(DIHE)=0.000 E(IMPR)=111.947 E(VDW )=-258.921 E(ELEC)=-136.999 | | E(CDIH)=1.576 E(NOE )=55.183 E(PLAN)=13.633 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61383 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61275 intra-atom interactions NBONDS: found 61269 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61303 intra-atom interactions NBONDS: found 61331 intra-atom interactions NBONDS: found 61351 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61446 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=932.912 E(kin)=605.108 temperature=299.856 | | Etotal =327.804 grad(E)=68.389 E(BOND)=231.525 E(ANGL)=326.857 | | E(DIHE)=0.000 E(IMPR)=93.656 E(VDW )=-258.744 E(ELEC)=-149.184 | | E(CDIH)=1.138 E(NOE )=65.093 E(PLAN)=17.463 | ------------------------------------------------------------------------------- NBONDS: found 61509 intra-atom interactions NBONDS: found 61531 intra-atom interactions NBONDS: found 61502 intra-atom interactions NBONDS: found 61471 intra-atom interactions NBONDS: found 61447 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61409 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61399 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=928.686 E(kin)=592.012 temperature=293.367 | | Etotal =336.674 grad(E)=68.596 E(BOND)=211.904 E(ANGL)=345.030 | | E(DIHE)=0.000 E(IMPR)=104.827 E(VDW )=-264.563 E(ELEC)=-137.836 | | E(CDIH)=1.412 E(NOE )=63.750 E(PLAN)=12.150 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61313 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61317 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61318 intra-atom interactions NBONDS: found 61325 intra-atom interactions NBONDS: found 61348 intra-atom interactions NBONDS: found 61408 intra-atom interactions NBONDS: found 61442 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=930.537 E(kin)=599.454 temperature=297.055 | | Etotal =331.084 grad(E)=70.666 E(BOND)=210.516 E(ANGL)=345.989 | | E(DIHE)=0.000 E(IMPR)=104.744 E(VDW )=-261.234 E(ELEC)=-139.121 | | E(CDIH)=1.160 E(NOE )=52.473 E(PLAN)=16.556 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61450 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61490 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61495 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61553 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61627 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61682 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61752 intra-atom interactions NBONDS: found 61856 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=954.193 E(kin)=615.812 temperature=305.161 | | Etotal =338.381 grad(E)=67.601 E(BOND)=198.582 E(ANGL)=354.928 | | E(DIHE)=0.000 E(IMPR)=101.288 E(VDW )=-265.319 E(ELEC)=-135.266 | | E(CDIH)=1.441 E(NOE )=65.021 E(PLAN)=17.706 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61880 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61885 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61882 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61915 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61912 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61877 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=929.354 E(kin)=588.506 temperature=291.630 | | Etotal =340.848 grad(E)=72.006 E(BOND)=224.240 E(ANGL)=355.107 | | E(DIHE)=0.000 E(IMPR)=93.852 E(VDW )=-260.484 E(ELEC)=-144.405 | | E(CDIH)=4.184 E(NOE )=52.770 E(PLAN)=15.583 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61938 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61964 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61950 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61920 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62008 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62007 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62018 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=937.320 E(kin)=627.440 temperature=310.923 | | Etotal =309.880 grad(E)=68.671 E(BOND)=206.585 E(ANGL)=342.456 | | E(DIHE)=0.000 E(IMPR)=86.709 E(VDW )=-262.263 E(ELEC)=-146.937 | | E(CDIH)=2.403 E(NOE )=63.994 E(PLAN)=16.933 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=933.178 E(kin)=605.514 temperature=300.058 | | Etotal =327.664 grad(E)=69.601 E(BOND)=219.992 E(ANGL)=338.431 | | E(DIHE)=0.000 E(IMPR)=96.090 E(VDW )=-260.890 E(ELEC)=-141.050 | | E(CDIH)=1.849 E(NOE )=57.705 E(PLAN)=15.535 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.205 E(kin)=12.985 temperature=6.435 | | Etotal =16.252 grad(E)=1.882 E(BOND)=10.155 E(ANGL)=11.797 | | E(DIHE)=0.000 E(IMPR)=7.667 E(VDW )=4.448 E(ELEC)=4.921 | | E(CDIH)=1.153 E(NOE )=6.200 E(PLAN)=1.587 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=933.016 E(kin)=605.335 temperature=299.969 | | Etotal =327.682 grad(E)=67.697 E(BOND)=211.218 E(ANGL)=337.517 | | E(DIHE)=0.000 E(IMPR)=93.568 E(VDW )=-261.109 E(ELEC)=-135.066 | | E(CDIH)=2.071 E(NOE )=63.680 E(PLAN)=15.803 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=15.514 E(kin)=13.560 temperature=6.720 | | Etotal =17.856 grad(E)=2.483 E(BOND)=11.287 E(ANGL)=12.271 | | E(DIHE)=0.000 E(IMPR)=7.879 E(VDW )=5.718 E(ELEC)=7.563 | | E(CDIH)=1.418 E(NOE )=7.997 E(PLAN)=1.909 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62054 intra-atom interactions NBONDS: found 62076 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62081 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62081 intra-atom interactions NBONDS: found 62057 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62071 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=916.478 E(kin)=600.200 temperature=297.424 | | Etotal =316.278 grad(E)=65.520 E(BOND)=219.709 E(ANGL)=332.989 | | E(DIHE)=0.000 E(IMPR)=98.603 E(VDW )=-264.895 E(ELEC)=-146.300 | | E(CDIH)=3.408 E(NOE )=56.825 E(PLAN)=15.938 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62013 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61947 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61909 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61997 intra-atom interactions NBONDS: found 62000 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.50 A apart NBONDS: found 62098 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=920.270 E(kin)=612.691 temperature=303.614 | | Etotal =307.579 grad(E)=68.216 E(BOND)=207.477 E(ANGL)=338.079 | | E(DIHE)=0.000 E(IMPR)=93.643 E(VDW )=-261.993 E(ELEC)=-144.032 | | E(CDIH)=3.032 E(NOE )=58.866 E(PLAN)=12.507 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62206 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62313 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62359 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62436 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62518 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62502 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62500 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=909.673 E(kin)=603.354 temperature=298.987 | | Etotal =306.318 grad(E)=70.887 E(BOND)=217.339 E(ANGL)=352.991 | | E(DIHE)=0.000 E(IMPR)=93.885 E(VDW )=-272.311 E(ELEC)=-148.973 | | E(CDIH)=0.250 E(NOE )=48.911 E(PLAN)=14.227 | ------------------------------------------------------------------------------- NBONDS: found 62457 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62340 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62237 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62186 intra-atom interactions NBONDS: found 62124 intra-atom interactions NBONDS: found 62024 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=925.366 E(kin)=597.680 temperature=296.176 | | Etotal =327.686 grad(E)=72.611 E(BOND)=204.823 E(ANGL)=341.442 | | E(DIHE)=0.000 E(IMPR)=107.692 E(VDW )=-269.703 E(ELEC)=-145.416 | | E(CDIH)=2.054 E(NOE )=67.600 E(PLAN)=19.196 | ------------------------------------------------------------------------------- NBONDS: found 61998 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61946 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61895 intra-atom interactions NBONDS: found 61864 intra-atom interactions NBONDS: found 61936 intra-atom interactions NBONDS: found 62029 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62088 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62180 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=931.971 E(kin)=609.453 temperature=302.009 | | Etotal =322.518 grad(E)=71.219 E(BOND)=231.004 E(ANGL)=340.133 | | E(DIHE)=0.000 E(IMPR)=91.300 E(VDW )=-273.402 E(ELEC)=-141.004 | | E(CDIH)=1.059 E(NOE )=55.891 E(PLAN)=17.537 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62260 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62299 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62353 intra-atom interactions NBONDS: found 62372 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62385 intra-atom interactions NBONDS: found 62354 intra-atom interactions NBONDS: found 62307 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=913.079 E(kin)=613.924 temperature=304.225 | | Etotal =299.156 grad(E)=66.999 E(BOND)=211.840 E(ANGL)=326.484 | | E(DIHE)=0.000 E(IMPR)=88.691 E(VDW )=-260.842 E(ELEC)=-145.152 | | E(CDIH)=0.421 E(NOE )=61.008 E(PLAN)=16.705 | ------------------------------------------------------------------------------- NBONDS: found 62248 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62223 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62180 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62237 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62246 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62260 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=930.611 E(kin)=620.453 temperature=307.460 | | Etotal =310.158 grad(E)=68.859 E(BOND)=210.935 E(ANGL)=325.161 | | E(DIHE)=0.000 E(IMPR)=108.584 E(VDW )=-255.432 E(ELEC)=-152.271 | | E(CDIH)=0.856 E(NOE )=55.438 E(PLAN)=16.888 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62256 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62233 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62205 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62173 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62077 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62068 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62010 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=931.428 E(kin)=592.097 temperature=293.409 | | Etotal =339.331 grad(E)=71.330 E(BOND)=239.517 E(ANGL)=323.918 | | E(DIHE)=0.000 E(IMPR)=102.226 E(VDW )=-254.630 E(ELEC)=-147.876 | | E(CDIH)=0.431 E(NOE )=60.234 E(PLAN)=15.510 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61933 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61950 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61944 intra-atom interactions NBONDS: found 61923 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61927 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61943 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61958 intra-atom interactions NBONDS: found 62058 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=930.654 E(kin)=612.948 temperature=303.742 | | Etotal =317.705 grad(E)=66.729 E(BOND)=206.201 E(ANGL)=333.009 | | E(DIHE)=0.000 E(IMPR)=95.871 E(VDW )=-259.949 E(ELEC)=-139.666 | | E(CDIH)=1.755 E(NOE )=65.766 E(PLAN)=14.719 | ------------------------------------------------------------------------------- NBONDS: found 62120 intra-atom interactions NBONDS: found 62235 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62245 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62321 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62298 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62360 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62321 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62325 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=939.093 E(kin)=606.820 temperature=300.705 | | Etotal =332.273 grad(E)=74.677 E(BOND)=223.118 E(ANGL)=330.573 | | E(DIHE)=0.000 E(IMPR)=108.078 E(VDW )=-258.459 E(ELEC)=-141.862 | | E(CDIH)=1.109 E(NOE )=54.082 E(PLAN)=15.635 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=928.758 E(kin)=605.508 temperature=300.055 | | Etotal =323.251 grad(E)=69.885 E(BOND)=218.805 E(ANGL)=336.288 | | E(DIHE)=0.000 E(IMPR)=98.186 E(VDW )=-262.510 E(ELEC)=-145.171 | | E(CDIH)=1.777 E(NOE )=60.046 E(PLAN)=15.831 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.053 E(kin)=13.202 temperature=6.542 | | Etotal =15.121 grad(E)=1.811 E(BOND)=10.136 E(ANGL)=11.828 | | E(DIHE)=0.000 E(IMPR)=7.223 E(VDW )=5.393 E(ELEC)=3.448 | | E(CDIH)=1.075 E(NOE )=5.685 E(PLAN)=2.039 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=932.733 E(kin)=605.346 temperature=299.974 | | Etotal =327.386 grad(E)=67.843 E(BOND)=211.724 E(ANGL)=337.435 | | E(DIHE)=0.000 E(IMPR)=93.876 E(VDW )=-261.202 E(ELEC)=-135.740 | | E(CDIH)=2.051 E(NOE )=63.438 E(PLAN)=15.805 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=15.168 E(kin)=13.537 temperature=6.708 | | Etotal =17.722 grad(E)=2.504 E(BOND)=11.373 E(ANGL)=12.246 | | E(DIHE)=0.000 E(IMPR)=7.921 E(VDW )=5.707 E(ELEC)=7.780 | | E(CDIH)=1.400 E(NOE )=7.916 E(PLAN)=1.918 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62272 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62246 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62136 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62008 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61901 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61862 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61842 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61849 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=951.989 E(kin)=611.570 temperature=303.059 | | Etotal =340.419 grad(E)=71.610 E(BOND)=215.589 E(ANGL)=346.603 | | E(DIHE)=0.000 E(IMPR)=104.984 E(VDW )=-259.054 E(ELEC)=-137.083 | | E(CDIH)=5.578 E(NOE )=48.052 E(PLAN)=15.750 | ------------------------------------------------------------------------------- NBONDS: found 61938 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart NBONDS: found 62033 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62128 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62202 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62268 intra-atom interactions NBONDS: found 62330 intra-atom interactions NBONDS: found 62364 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=926.100 E(kin)=589.676 temperature=292.209 | | Etotal =336.425 grad(E)=70.009 E(BOND)=233.423 E(ANGL)=343.274 | | E(DIHE)=0.000 E(IMPR)=88.917 E(VDW )=-262.587 E(ELEC)=-142.003 | | E(CDIH)=0.986 E(NOE )=60.326 E(PLAN)=14.088 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62450 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62545 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62565 intra-atom interactions NBONDS: found 62616 intra-atom interactions NBONDS: found 62496 intra-atom interactions NBONDS: found 62489 intra-atom interactions NBONDS: found 62461 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=932.277 E(kin)=593.580 temperature=294.144 | | Etotal =338.696 grad(E)=70.898 E(BOND)=214.932 E(ANGL)=355.613 | | E(DIHE)=0.000 E(IMPR)=93.537 E(VDW )=-262.652 E(ELEC)=-135.783 | | E(CDIH)=1.075 E(NOE )=55.683 E(PLAN)=16.291 | ------------------------------------------------------------------------------- NBONDS: found 62433 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62470 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62486 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62491 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62526 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62586 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62647 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62599 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62613 intra-atom interactions NBONDS: found 62579 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=933.679 E(kin)=610.238 temperature=302.398 | | Etotal =323.442 grad(E)=67.359 E(BOND)=222.193 E(ANGL)=341.627 | | E(DIHE)=0.000 E(IMPR)=87.950 E(VDW )=-265.230 E(ELEC)=-142.771 | | E(CDIH)=0.122 E(NOE )=65.680 E(PLAN)=13.872 | ------------------------------------------------------------------------------- NBONDS: found 62572 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62578 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62504 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62505 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62490 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62481 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62479 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62467 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.41 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62492 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62474 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=931.098 E(kin)=600.300 temperature=297.474 | | Etotal =330.798 grad(E)=71.909 E(BOND)=217.418 E(ANGL)=353.637 | | E(DIHE)=0.000 E(IMPR)=91.613 E(VDW )=-257.542 E(ELEC)=-141.697 | | E(CDIH)=2.316 E(NOE )=52.050 E(PLAN)=13.002 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62446 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62419 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62358 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62343 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62326 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62295 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62240 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62254 intra-atom interactions NBONDS: found 62253 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=928.145 E(kin)=588.777 temperature=291.764 | | Etotal =339.368 grad(E)=72.732 E(BOND)=223.974 E(ANGL)=345.827 | | E(DIHE)=0.000 E(IMPR)=93.603 E(VDW )=-260.916 E(ELEC)=-138.597 | | E(CDIH)=2.540 E(NOE )=61.643 E(PLAN)=11.294 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62259 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 62265 intra-atom interactions NBONDS: found 62296 intra-atom interactions NBONDS: found 62311 intra-atom interactions NBONDS: found 62341 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62327 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62300 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62300 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=929.769 E(kin)=595.238 temperature=294.965 | | Etotal =334.531 grad(E)=70.047 E(BOND)=225.437 E(ANGL)=355.204 | | E(DIHE)=0.000 E(IMPR)=93.918 E(VDW )=-265.586 E(ELEC)=-139.959 | | E(CDIH)=1.057 E(NOE )=53.446 E(PLAN)=11.015 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62325 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62307 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62272 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62292 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62294 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62342 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62355 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62336 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62232 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=955.994 E(kin)=601.721 temperature=298.178 | | Etotal =354.273 grad(E)=72.468 E(BOND)=212.080 E(ANGL)=359.499 | | E(DIHE)=0.000 E(IMPR)=102.982 E(VDW )=-268.915 E(ELEC)=-135.822 | | E(CDIH)=3.172 E(NOE )=63.336 E(PLAN)=17.942 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62181 intra-atom interactions NBONDS: found 62175 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62120 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62037 intra-atom interactions NBONDS: found 62028 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62006 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61993 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62011 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart NBONDS: found 62001 intra-atom interactions NBONDS: found 62016 intra-atom interactions NBONDS: found 62054 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=936.917 E(kin)=614.749 temperature=304.634 | | Etotal =322.167 grad(E)=68.000 E(BOND)=217.964 E(ANGL)=338.151 | | E(DIHE)=0.000 E(IMPR)=85.152 E(VDW )=-263.792 E(ELEC)=-138.536 | | E(CDIH)=1.292 E(NOE )=64.169 E(PLAN)=17.767 | ------------------------------------------------------------------------------- NBONDS: found 62056 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.43 A apart NBONDS: found 62062 intra-atom interactions NBONDS: found 61984 intra-atom interactions NBONDS: found 61956 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61911 intra-atom interactions NBONDS: found 61934 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61944 intra-atom interactions NBONDS: found 61856 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=922.189 E(kin)=601.405 temperature=298.021 | | Etotal =320.784 grad(E)=71.039 E(BOND)=228.627 E(ANGL)=333.160 | | E(DIHE)=0.000 E(IMPR)=91.524 E(VDW )=-258.800 E(ELEC)=-146.879 | | E(CDIH)=1.163 E(NOE )=56.164 E(PLAN)=15.825 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=935.735 E(kin)=605.578 temperature=300.089 | | Etotal =330.156 grad(E)=70.360 E(BOND)=218.922 E(ANGL)=341.606 | | E(DIHE)=0.000 E(IMPR)=94.568 E(VDW )=-261.670 E(ELEC)=-139.878 | | E(CDIH)=1.827 E(NOE )=59.532 E(PLAN)=15.249 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.704 E(kin)=13.182 temperature=6.532 | | Etotal =16.194 grad(E)=2.013 E(BOND)=10.563 E(ANGL)=11.776 | | E(DIHE)=0.000 E(IMPR)=7.653 E(VDW )=4.799 E(ELEC)=3.875 | | E(CDIH)=1.279 E(NOE )=5.431 E(PLAN)=1.944 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=932.920 E(kin)=605.361 temperature=299.982 | | Etotal =327.560 grad(E)=68.000 E(BOND)=212.174 E(ANGL)=337.695 | | E(DIHE)=0.000 E(IMPR)=93.919 E(VDW )=-261.231 E(ELEC)=-135.999 | | E(CDIH)=2.037 E(NOE )=63.194 E(PLAN)=15.770 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=14.904 E(kin)=13.515 temperature=6.697 | | Etotal =17.643 grad(E)=2.550 E(BOND)=11.457 E(ANGL)=12.259 | | E(DIHE)=0.000 E(IMPR)=7.906 E(VDW )=5.656 E(ELEC)=7.661 | | E(CDIH)=1.394 E(NOE )=7.841 E(PLAN)=1.925 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.05645 0.04692 0.01980 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:16-Aug-96 21:44:55 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 -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62075 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62075 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62074 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =-216.579 grad(E)=9.962 E(BOND)=23.884 E(ANGL)=117.874 | | E(DIHE)=0.000 E(IMPR)=14.786 E(VDW )=-264.075 E(ELEC)=-149.826 | | E(CDIH)=0.245 E(NOE )=26.926 E(PLAN)=13.607 | ------------------------------------------------------------------------------- %atoms "A -1 -GUA -H5T " and "A -1 -GUA -H5''" only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62066 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =-269.812 grad(E)=4.375 E(BOND)=8.815 E(ANGL)=80.676 | | E(DIHE)=0.000 E(IMPR)=13.465 E(VDW )=-265.817 E(ELEC)=-148.166 | | E(CDIH)=0.304 E(NOE )=28.025 E(PLAN)=12.886 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =-283.284 grad(E)=1.972 E(BOND)=7.037 E(ANGL)=75.652 | | E(DIHE)=0.000 E(IMPR)=12.763 E(VDW )=-270.003 E(ELEC)=-149.408 | | E(CDIH)=0.175 E(NOE )=28.071 E(PLAN)=12.430 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =-286.433 grad(E)=1.416 E(BOND)=6.924 E(ANGL)=75.321 | | E(DIHE)=0.000 E(IMPR)=12.652 E(VDW )=-271.684 E(ELEC)=-150.583 | | E(CDIH)=0.186 E(NOE )=28.687 E(PLAN)=12.066 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =-288.354 grad(E)=1.686 E(BOND)=6.747 E(ANGL)=74.944 | | E(DIHE)=0.000 E(IMPR)=12.871 E(VDW )=-272.144 E(ELEC)=-151.945 | | E(CDIH)=0.151 E(NOE )=29.375 E(PLAN)=11.648 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62070 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =-289.382 grad(E)=1.043 E(BOND)=6.822 E(ANGL)=75.269 | | E(DIHE)=0.000 E(IMPR)=12.753 E(VDW )=-272.553 E(ELEC)=-153.348 | | E(CDIH)=0.249 E(NOE )=30.060 E(PLAN)=11.366 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =-290.435 grad(E)=0.773 E(BOND)=6.772 E(ANGL)=76.116 | | E(DIHE)=0.000 E(IMPR)=12.749 E(VDW )=-272.758 E(ELEC)=-155.288 | | E(CDIH)=0.360 E(NOE )=30.393 E(PLAN)=11.220 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =-291.039 grad(E)=0.967 E(BOND)=6.822 E(ANGL)=75.928 | | E(DIHE)=0.000 E(IMPR)=12.960 E(VDW )=-272.878 E(ELEC)=-156.266 | | E(CDIH)=0.377 E(NOE )=30.787 E(PLAN)=11.231 | ------------------------------------------------------------------------------- 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= 0.002 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.212827E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. Number of violations greater 5.000: 0 RMS deviation= 0.637 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.637250 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 0.000000E+00 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.362 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.362077 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 12 URI H1' set-j-atoms A 13 ADE H8 R= 5.288 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.288 E(NOE)= 8.276 NOEPRI: RMS diff. = 0.018, #(violat.> 0.2)= 1 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.018, #(viol.> 0.2)= 1 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.182142E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 1.00000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 0 RMS deviation= 0.087 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.873093E-01 (real) X-PLOR>evaluate ($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 6.82185, angle 75.9282, dihedral 0, improper 12.9596, NOE 30.7869, c-dihedral 0.377104, planar 11.2312, VdW -272.878, elec -156.266, total -291.039 RMSD: bond 2.128274E-03, angle 0.63725, dihedral 0, improper 0.362077, NOE 1.821415E-02, c-dihedral 8.730925E-02 Violations: bond 0, angle 0, dihedral 0, improper 0, NOE 1, 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= 134787 current use= 0 X-PLOR: total CPU time= 2826.2832 s X-PLOR: entry time at 21:44:21 16-Aug-96 X-PLOR: exit time at 22:31:53 16-Aug-96