X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 07:12:25 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=25294.9051208496 SET> end ! Use 'xplor -s' X-PLOR> X-PLOR>set echo=off message=off end ! Normal use REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp" REMARKS DATE:27-Apr-96 13:37:21 created by user: XPLOR: current counts (number in parenthesis is maximum) NATOM= 677(MAXA= 96000) NBOND= 728(MAXB= 96000) NTHETA= 1299(MAXT= 144000) NGRP= 218(MAXGRP= 96000) NPHI= 0(MAXP= 180000) NIMPHI= 461(MAXIMP= 96000) NDON= 68(MAXPAD= 24000) NACC= 105(MAXPAD= 24000) NNB= 63(MAXNB= 18000) NOE: allocating space for 1000 restraints. XREFIN: allocating space for 300 assignments. X-PLOR> X-PLOR>noe ! Parameters for NOE effective energy term. NOE> ceiling=1000 NOE> averaging * cent NOE> potential * square NOE> sqconstant * 1 NOE> sqexponent * 2 NOE> scale * 100 ! Constant NOE scale throughout the protocol. NOE>end X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> ctonnb=9.5 NBDSET> ctofnb=10.5 NBDSET> cutnb=11.5 NBDSET> tolerance=0.5 NBDSET> rdie NBDSET> switch NBDSET> vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR>restraints dihedral scale=800 end X-PLOR> X-PLOR>coordinates @dgsa.pdb ! END in PDB file ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/dgsa.pdb opened. COOR>REMARK 5 FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/dgsa.pdb" COOR>REMARK 5 DATE:16-Aug-96 19:30:55 created by user: COOR>ATOM 1 P GUA A 1 -6.439 9.947 1.174 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -6.650 9.973 -0.296 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 -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61741 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =-214.564 grad(E)=3.708 E(BOND)=8.334 E(ANGL)=83.352 | | E(DIHE)=0.000 E(IMPR)=14.012 E(VDW )=-258.133 E(ELEC)=-105.043 | | E(CDIH)=0.240 E(NOE )=32.850 E(PLAN)=9.825 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =-227.195 grad(E)=2.655 E(BOND)=7.144 E(ANGL)=82.042 | | E(DIHE)=0.000 E(IMPR)=11.846 E(VDW )=-264.183 E(ELEC)=-108.073 | | E(CDIH)=0.268 E(NOE )=32.575 E(PLAN)=11.187 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =-235.999 grad(E)=3.144 E(BOND)=6.325 E(ANGL)=80.100 | | E(DIHE)=0.000 E(IMPR)=13.851 E(VDW )=-264.684 E(ELEC)=-113.505 | | E(CDIH)=0.450 E(NOE )=30.029 E(PLAN)=11.435 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =-245.276 grad(E)=2.380 E(BOND)=7.520 E(ANGL)=80.550 | | E(DIHE)=0.000 E(IMPR)=14.342 E(VDW )=-269.320 E(ELEC)=-122.711 | | E(CDIH)=0.444 E(NOE )=31.736 E(PLAN)=12.161 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =-252.160 grad(E)=2.413 E(BOND)=7.790 E(ANGL)=80.235 | | E(DIHE)=0.000 E(IMPR)=14.090 E(VDW )=-270.130 E(ELEC)=-129.845 | | E(CDIH)=0.512 E(NOE )=32.392 E(PLAN)=12.797 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61970 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =-257.063 grad(E)=2.383 E(BOND)=7.824 E(ANGL)=81.284 | | E(DIHE)=0.000 E(IMPR)=13.342 E(VDW )=-271.163 E(ELEC)=-134.328 | | E(CDIH)=0.460 E(NOE )=32.554 E(PLAN)=12.963 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =-260.428 grad(E)=2.093 E(BOND)=7.533 E(ANGL)=80.524 | | E(DIHE)=0.000 E(IMPR)=12.903 E(VDW )=-270.874 E(ELEC)=-136.548 | | E(CDIH)=0.589 E(NOE )=32.642 E(PLAN)=12.803 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =-263.250 grad(E)=1.251 E(BOND)=7.732 E(ANGL)=80.471 | | E(DIHE)=0.000 E(IMPR)=12.611 E(VDW )=-271.147 E(ELEC)=-138.670 | | E(CDIH)=0.714 E(NOE )=32.662 E(PLAN)=12.377 | ------------------------------------------------------------------------------- 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= 0.195588587E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.07379 0.04041 0.01162 velocity [A/ps] : -0.23889 -0.02349 0.15982 ang. mom. [amu A/ps] : -3348.49227 -8591.92830 -24805.39692 kin. ener. [Kcal/mol] : 0.67032 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.07379 0.04041 0.01162 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)=317.411 E(kin)=580.661 temperature=287.742 | | Etotal =-263.250 grad(E)=1.251 E(BOND)=7.732 E(ANGL)=80.471 | | E(DIHE)=0.000 E(IMPR)=12.611 E(VDW )=-271.147 E(ELEC)=-138.670 | | E(CDIH)=0.714 E(NOE )=32.662 E(PLAN)=12.377 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62136 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.44 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62186 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.47 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62230 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62269 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62316 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.43 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62321 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart NBONDS: found 62345 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62325 intra-atom interactions %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 1.48 A apart NBONDS: found 62357 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62380 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.45 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62370 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62323 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 1.46 A apart NBONDS: found 62329 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=937.225 E(kin)=582.828 temperature=288.816 | | Etotal =354.397 grad(E)=68.183 E(BOND)=222.030 E(ANGL)=340.780 | | E(DIHE)=0.000 E(IMPR)=93.453 E(VDW )=-254.713 E(ELEC)=-134.159 | | E(CDIH)=1.574 E(NOE )=69.700 E(PLAN)=15.732 | ------------------------------------------------------------------------------- %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 62285 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62293 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 62307 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 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 62343 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62334 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62317 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62261 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62195 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=912.059 E(kin)=615.250 temperature=304.882 | | Etotal =296.809 grad(E)=65.176 E(BOND)=199.065 E(ANGL)=333.108 | | E(DIHE)=0.000 E(IMPR)=82.356 E(VDW )=-258.212 E(ELEC)=-140.509 | | E(CDIH)=0.828 E(NOE )=61.823 E(PLAN)=18.350 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62163 intra-atom interactions NBONDS: found 62115 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 1.46 A apart NBONDS: found 62093 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 1.49 A apart NBONDS: found 62149 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 1.47 A apart NBONDS: found 62173 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 62174 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 62191 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 62235 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=928.993 E(kin)=635.973 temperature=315.151 | | Etotal =293.020 grad(E)=63.974 E(BOND)=193.688 E(ANGL)=323.656 | | E(DIHE)=0.000 E(IMPR)=84.099 E(VDW )=-259.903 E(ELEC)=-132.933 | | E(CDIH)=0.980 E(NOE )=64.314 E(PLAN)=19.118 | ------------------------------------------------------------------------------- %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 1.42 A apart NBONDS: found 62202 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 1.43 A apart NBONDS: found 62217 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 62190 intra-atom interactions NBONDS: found 62145 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62091 intra-atom interactions NBONDS: found 61962 intra-atom interactions NBONDS: found 61856 intra-atom interactions NBONDS: found 61815 intra-atom interactions NBONDS: found 61825 intra-atom interactions NBONDS: found 61787 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=927.645 E(kin)=570.876 temperature=282.893 | | Etotal =356.769 grad(E)=68.860 E(BOND)=216.404 E(ANGL)=318.241 | | E(DIHE)=0.000 E(IMPR)=100.990 E(VDW )=-250.087 E(ELEC)=-121.672 | | E(CDIH)=3.191 E(NOE )=75.308 E(PLAN)=14.394 | ------------------------------------------------------------------------------- NBONDS: found 61857 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61896 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61920 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61983 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62058 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 62150 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 62189 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 %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62216 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 62258 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=899.233 E(kin)=602.170 temperature=298.401 | | Etotal =297.063 grad(E)=63.882 E(BOND)=202.847 E(ANGL)=316.451 | | E(DIHE)=0.000 E(IMPR)=89.190 E(VDW )=-257.351 E(ELEC)=-142.670 | | E(CDIH)=1.135 E(NOE )=71.538 E(PLAN)=15.923 | ------------------------------------------------------------------------------- %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 62230 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62191 intra-atom interactions NBONDS: found 62108 intra-atom interactions NBONDS: found 62054 intra-atom interactions NBONDS: found 61995 intra-atom interactions NBONDS: found 61979 intra-atom interactions NBONDS: found 62022 intra-atom interactions NBONDS: found 62054 intra-atom interactions NBONDS: found 62036 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=925.630 E(kin)=596.870 temperature=295.774 | | Etotal =328.760 grad(E)=65.212 E(BOND)=195.990 E(ANGL)=340.923 | | E(DIHE)=0.000 E(IMPR)=80.590 E(VDW )=-259.117 E(ELEC)=-129.336 | | E(CDIH)=1.997 E(NOE )=80.738 E(PLAN)=16.975 | ------------------------------------------------------------------------------- NBONDS: found 62044 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 62089 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 1.45 A apart NBONDS: found 62105 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 1.46 A apart NBONDS: found 62153 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 1.40 A apart NBONDS: found 62288 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 1.47 A apart NBONDS: found 62328 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62394 intra-atom interactions NBONDS: found 62428 intra-atom interactions NBONDS: found 62416 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=937.452 E(kin)=606.241 temperature=300.418 | | Etotal =331.211 grad(E)=66.245 E(BOND)=210.881 E(ANGL)=339.051 | | E(DIHE)=0.000 E(IMPR)=78.839 E(VDW )=-260.902 E(ELEC)=-128.134 | | E(CDIH)=3.068 E(NOE )=71.363 E(PLAN)=17.045 | ------------------------------------------------------------------------------- NBONDS: found 62428 intra-atom interactions NBONDS: found 62362 intra-atom interactions NBONDS: found 62312 intra-atom interactions NBONDS: found 62341 intra-atom interactions NBONDS: found 62367 intra-atom interactions NBONDS: found 62448 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62398 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=944.561 E(kin)=602.435 temperature=298.532 | | Etotal =342.126 grad(E)=67.989 E(BOND)=218.429 E(ANGL)=331.578 | | E(DIHE)=0.000 E(IMPR)=90.787 E(VDW )=-254.996 E(ELEC)=-133.506 | | E(CDIH)=0.980 E(NOE )=71.765 E(PLAN)=17.089 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62465 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62467 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62528 intra-atom interactions NBONDS: found 62608 intra-atom interactions NBONDS: found 62642 intra-atom interactions NBONDS: found 62671 intra-atom interactions NBONDS: found 62694 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=927.645 E(kin)=623.126 temperature=308.785 | | Etotal =304.518 grad(E)=65.368 E(BOND)=200.748 E(ANGL)=321.849 | | E(DIHE)=0.000 E(IMPR)=83.825 E(VDW )=-254.662 E(ELEC)=-126.580 | | E(CDIH)=1.188 E(NOE )=63.133 E(PLAN)=15.017 | ------------------------------------------------------------------------------- NBONDS: found 62782 intra-atom interactions NBONDS: found 62862 intra-atom interactions NBONDS: found 62884 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62853 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 62795 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=922.178 E(kin)=578.310 temperature=286.577 | | Etotal =343.869 grad(E)=68.729 E(BOND)=216.926 E(ANGL)=358.926 | | E(DIHE)=0.000 E(IMPR)=82.823 E(VDW )=-259.298 E(ELEC)=-139.716 | | E(CDIH)=0.001 E(NOE )=69.925 E(PLAN)=14.282 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=924.133 E(kin)=603.218 temperature=298.920 | | Etotal =320.915 grad(E)=66.208 E(BOND)=206.499 E(ANGL)=331.680 | | E(DIHE)=0.000 E(IMPR)=88.907 E(VDW )=-259.355 E(ELEC)=-133.216 | | E(CDIH)=2.053 E(NOE )=67.998 E(PLAN)=16.349 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=42.921 E(kin)=22.757 temperature=11.277 | | Etotal =30.423 grad(E)=1.924 E(BOND)=13.272 E(ANGL)=15.843 | | E(DIHE)=0.000 E(IMPR)=7.244 E(VDW )=6.743 E(ELEC)=5.940 | | E(CDIH)=1.356 E(NOE )=7.034 E(PLAN)=2.341 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62704 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 1.43 A apart NBONDS: found 62575 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 62451 intra-atom interactions NBONDS: found 62393 intra-atom interactions NBONDS: found 62472 intra-atom interactions NBONDS: found 62612 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=925.901 E(kin)=600.368 temperature=297.508 | | Etotal =325.532 grad(E)=66.526 E(BOND)=210.574 E(ANGL)=358.160 | | E(DIHE)=0.000 E(IMPR)=82.588 E(VDW )=-271.821 E(ELEC)=-131.902 | | E(CDIH)=1.717 E(NOE )=61.973 E(PLAN)=14.245 | ------------------------------------------------------------------------------- NBONDS: found 62712 intra-atom interactions NBONDS: found 62782 intra-atom interactions NBONDS: found 62827 intra-atom interactions NBONDS: found 62928 intra-atom interactions NBONDS: found 62887 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62784 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 62665 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62599 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=921.314 E(kin)=595.101 temperature=294.898 | | Etotal =326.213 grad(E)=68.236 E(BOND)=207.384 E(ANGL)=339.057 | | E(DIHE)=0.000 E(IMPR)=91.461 E(VDW )=-268.171 E(ELEC)=-129.781 | | E(CDIH)=2.594 E(NOE )=65.376 E(PLAN)=18.293 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62598 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62646 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62660 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62649 intra-atom interactions NBONDS: found 62578 intra-atom interactions NBONDS: found 62553 intra-atom interactions NBONDS: found 62593 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=929.180 E(kin)=620.577 temperature=307.522 | | Etotal =308.603 grad(E)=66.624 E(BOND)=203.353 E(ANGL)=334.739 | | E(DIHE)=0.000 E(IMPR)=89.813 E(VDW )=-261.947 E(ELEC)=-147.085 | | E(CDIH)=4.523 E(NOE )=69.384 E(PLAN)=15.823 | ------------------------------------------------------------------------------- NBONDS: found 62557 intra-atom interactions NBONDS: found 62574 intra-atom interactions NBONDS: found 62563 intra-atom interactions NBONDS: found 62543 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.47 A apart NBONDS: found 62551 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62620 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62621 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62592 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=928.571 E(kin)=584.817 temperature=289.801 | | Etotal =343.754 grad(E)=68.953 E(BOND)=212.808 E(ANGL)=347.377 | | E(DIHE)=0.000 E(IMPR)=92.288 E(VDW )=-259.200 E(ELEC)=-137.939 | | E(CDIH)=4.690 E(NOE )=65.754 E(PLAN)=17.977 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62630 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62626 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 -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62761 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.48 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62797 intra-atom interactions NBONDS: found 62869 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62940 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=925.603 E(kin)=606.365 temperature=300.479 | | Etotal =319.239 grad(E)=64.751 E(BOND)=225.681 E(ANGL)=323.787 | | E(DIHE)=0.000 E(IMPR)=80.402 E(VDW )=-264.888 E(ELEC)=-137.548 | | E(CDIH)=1.286 E(NOE )=72.814 E(PLAN)=17.705 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.40 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62949 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62994 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 1.45 A apart NBONDS: found 63052 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 1.50 A apart NBONDS: found 63023 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 1.45 A apart NBONDS: found 62951 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62935 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=938.323 E(kin)=587.587 temperature=291.174 | | Etotal =350.736 grad(E)=69.145 E(BOND)=207.042 E(ANGL)=358.724 | | E(DIHE)=0.000 E(IMPR)=108.272 E(VDW )=-265.380 E(ELEC)=-143.110 | | E(CDIH)=1.215 E(NOE )=65.741 E(PLAN)=18.233 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62894 intra-atom interactions NBONDS: found 62856 intra-atom interactions NBONDS: found 62842 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62751 intra-atom interactions NBONDS: found 62622 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62521 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62477 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=931.783 E(kin)=600.703 temperature=297.673 | | Etotal =331.080 grad(E)=66.707 E(BOND)=218.619 E(ANGL)=338.203 | | E(DIHE)=0.000 E(IMPR)=92.516 E(VDW )=-264.337 E(ELEC)=-141.385 | | E(CDIH)=0.597 E(NOE )=69.470 E(PLAN)=17.397 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62475 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62428 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62365 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62428 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62348 intra-atom interactions NBONDS: found 62251 intra-atom interactions NBONDS: found 62163 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=923.893 E(kin)=611.222 temperature=302.886 | | Etotal =312.671 grad(E)=66.044 E(BOND)=206.735 E(ANGL)=338.302 | | E(DIHE)=0.000 E(IMPR)=83.332 E(VDW )=-267.593 E(ELEC)=-134.983 | | E(CDIH)=1.188 E(NOE )=68.455 E(PLAN)=17.235 | ------------------------------------------------------------------------------- NBONDS: found 62168 intra-atom interactions NBONDS: found 62135 intra-atom interactions NBONDS: found 62099 intra-atom interactions NBONDS: found 62133 intra-atom interactions NBONDS: found 62135 intra-atom interactions NBONDS: found 62112 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart NBONDS: found 62077 intra-atom interactions NBONDS: found 62041 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 62009 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=932.674 E(kin)=592.190 temperature=293.455 | | Etotal =340.484 grad(E)=66.391 E(BOND)=220.989 E(ANGL)=332.665 | | E(DIHE)=0.000 E(IMPR)=94.493 E(VDW )=-261.939 E(ELEC)=-130.698 | | E(CDIH)=0.067 E(NOE )=67.343 E(PLAN)=17.565 | ------------------------------------------------------------------------------- %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 61965 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 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 61838 intra-atom interactions NBONDS: found 61833 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 61836 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61842 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61845 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61939 intra-atom interactions NBONDS: found 61932 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=928.046 E(kin)=604.562 temperature=299.586 | | Etotal =323.484 grad(E)=64.465 E(BOND)=201.656 E(ANGL)=334.750 | | E(DIHE)=0.000 E(IMPR)=93.633 E(VDW )=-266.152 E(ELEC)=-126.107 | | E(CDIH)=1.333 E(NOE )=67.370 E(PLAN)=17.001 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=928.654 E(kin)=605.464 temperature=300.033 | | Etotal =323.190 grad(E)=66.503 E(BOND)=210.708 E(ANGL)=336.630 | | E(DIHE)=0.000 E(IMPR)=91.089 E(VDW )=-265.201 E(ELEC)=-136.731 | | E(CDIH)=1.887 E(NOE )=68.557 E(PLAN)=16.251 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.501 E(kin)=12.024 temperature=5.958 | | Etotal =14.306 grad(E)=1.334 E(BOND)=9.432 E(ANGL)=11.175 | | E(DIHE)=0.000 E(IMPR)=6.979 E(VDW )=4.920 E(ELEC)=5.903 | | E(CDIH)=1.301 E(NOE )=6.600 E(PLAN)=2.437 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=926.393 E(kin)=604.341 temperature=299.476 | | Etotal =322.053 grad(E)=66.355 E(BOND)=208.603 E(ANGL)=334.155 | | E(DIHE)=0.000 E(IMPR)=89.998 E(VDW )=-262.278 E(ELEC)=-134.973 | | E(CDIH)=1.970 E(NOE )=68.277 E(PLAN)=16.300 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=31.022 E(kin)=18.234 temperature=9.036 | | Etotal =23.799 grad(E)=1.662 E(BOND)=11.704 E(ANGL)=13.931 | | E(DIHE)=0.000 E(IMPR)=7.196 E(VDW )=6.586 E(ELEC)=6.177 | | E(CDIH)=1.331 E(NOE )=6.827 E(PLAN)=2.390 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61929 intra-atom interactions NBONDS: found 61981 intra-atom interactions NBONDS: found 62022 intra-atom interactions NBONDS: found 62008 intra-atom interactions NBONDS: found 62022 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 1.48 A apart NBONDS: found 62050 intra-atom interactions %atoms "A -9 -URI -O5' " and "A -9 -URI -H6 " only 1.49 A apart NBONDS: found 62032 intra-atom interactions NBONDS: found 62042 intra-atom interactions NBONDS: found 62059 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=924.933 E(kin)=619.782 temperature=307.128 | | Etotal =305.151 grad(E)=65.063 E(BOND)=196.585 E(ANGL)=335.549 | | E(DIHE)=0.000 E(IMPR)=90.620 E(VDW )=-265.624 E(ELEC)=-136.943 | | E(CDIH)=3.706 E(NOE )=61.244 E(PLAN)=20.016 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62024 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 61973 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 61959 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 61930 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 1.40 A apart NBONDS: found 61835 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 1.40 A apart NBONDS: found 61751 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 1.41 A apart NBONDS: found 61795 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 61821 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=902.597 E(kin)=596.545 temperature=295.613 | | Etotal =306.052 grad(E)=65.445 E(BOND)=211.578 E(ANGL)=331.550 | | E(DIHE)=0.000 E(IMPR)=86.005 E(VDW )=-259.874 E(ELEC)=-138.467 | | E(CDIH)=1.263 E(NOE )=57.617 E(PLAN)=16.379 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61913 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61957 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62011 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61990 intra-atom interactions NBONDS: found 61973 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61906 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61876 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 61848 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61744 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 61718 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=932.823 E(kin)=613.860 temperature=304.193 | | Etotal =318.962 grad(E)=64.176 E(BOND)=202.630 E(ANGL)=322.669 | | E(DIHE)=0.000 E(IMPR)=101.005 E(VDW )=-249.858 E(ELEC)=-137.760 | | E(CDIH)=0.405 E(NOE )=63.183 E(PLAN)=16.689 | ------------------------------------------------------------------------------- %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 1.38 A apart NBONDS: found 61673 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 1.44 A apart NBONDS: found 61621 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61550 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61615 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61655 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61671 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61721 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61771 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=940.544 E(kin)=615.150 temperature=304.833 | | Etotal =325.394 grad(E)=65.455 E(BOND)=207.392 E(ANGL)=321.196 | | E(DIHE)=0.000 E(IMPR)=96.520 E(VDW )=-262.257 E(ELEC)=-132.972 | | E(CDIH)=0.956 E(NOE )=77.801 E(PLAN)=16.757 | ------------------------------------------------------------------------------- %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 61811 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61841 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61857 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 61860 intra-atom interactions NBONDS: found 61855 intra-atom interactions NBONDS: found 61886 intra-atom interactions NBONDS: found 61861 intra-atom interactions NBONDS: found 61866 intra-atom interactions NBONDS: found 61833 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=951.378 E(kin)=612.337 temperature=303.439 | | Etotal =339.040 grad(E)=67.250 E(BOND)=206.377 E(ANGL)=342.167 | | E(DIHE)=0.000 E(IMPR)=93.369 E(VDW )=-255.413 E(ELEC)=-137.786 | | E(CDIH)=1.089 E(NOE )=75.094 E(PLAN)=14.144 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61869 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61965 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 61969 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 1.38 A apart NBONDS: found 61968 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 61882 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 1.49 A apart NBONDS: found 61965 intra-atom interactions NBONDS: found 61943 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=939.026 E(kin)=609.889 temperature=302.226 | | Etotal =329.137 grad(E)=65.850 E(BOND)=213.211 E(ANGL)=346.717 | | E(DIHE)=0.000 E(IMPR)=89.344 E(VDW )=-249.243 E(ELEC)=-139.261 | | E(CDIH)=0.615 E(NOE )=52.986 E(PLAN)=14.768 | ------------------------------------------------------------------------------- NBONDS: found 61990 intra-atom interactions NBONDS: found 62000 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62083 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62114 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.37 A apart NBONDS: found 62097 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62128 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=940.097 E(kin)=595.205 temperature=294.949 | | Etotal =344.892 grad(E)=69.070 E(BOND)=223.554 E(ANGL)=356.120 | | E(DIHE)=0.000 E(IMPR)=97.396 E(VDW )=-258.368 E(ELEC)=-142.353 | | E(CDIH)=0.489 E(NOE )=51.693 E(PLAN)=16.360 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62093 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 62073 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 62090 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61981 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61977 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61931 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61911 intra-atom interactions NBONDS: found 61914 intra-atom interactions NBONDS: found 61876 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61841 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=924.859 E(kin)=589.075 temperature=291.911 | | Etotal =335.784 grad(E)=68.866 E(BOND)=218.764 E(ANGL)=342.534 | | E(DIHE)=0.000 E(IMPR)=90.918 E(VDW )=-257.031 E(ELEC)=-138.735 | | E(CDIH)=0.811 E(NOE )=62.750 E(PLAN)=15.774 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61812 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61786 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61741 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61725 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart NBONDS: found 61749 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart NBONDS: found 61780 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart NBONDS: found 61817 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart NBONDS: found 61859 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61941 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 61936 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=943.109 E(kin)=587.992 temperature=291.375 | | Etotal =355.117 grad(E)=68.638 E(BOND)=229.374 E(ANGL)=337.576 | | E(DIHE)=0.000 E(IMPR)=89.507 E(VDW )=-253.293 E(ELEC)=-141.403 | | E(CDIH)=5.567 E(NOE )=70.552 E(PLAN)=17.237 | ------------------------------------------------------------------------------- %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 61965 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 1.43 A apart NBONDS: found 61972 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 1.41 A apart NBONDS: found 61937 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 1.40 A apart NBONDS: found 61965 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 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61901 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 1.49 A apart NBONDS: found 61902 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61899 intra-atom interactions NBONDS: found 61914 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61922 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=924.389 E(kin)=604.506 temperature=299.558 | | Etotal =319.883 grad(E)=68.046 E(BOND)=214.584 E(ANGL)=320.439 | | E(DIHE)=0.000 E(IMPR)=85.753 E(VDW )=-253.830 E(ELEC)=-135.015 | | E(CDIH)=1.938 E(NOE )=68.312 E(PLAN)=17.700 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.615 E(kin)=605.497 temperature=300.049 | | Etotal =325.118 grad(E)=66.470 E(BOND)=214.166 E(ANGL)=335.959 | | E(DIHE)=0.000 E(IMPR)=89.439 E(VDW )=-258.819 E(ELEC)=-137.473 | | E(CDIH)=1.948 E(NOE )=63.531 E(PLAN)=16.367 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.501 E(kin)=12.472 temperature=6.180 | | Etotal =16.582 grad(E)=1.454 E(BOND)=10.586 E(ANGL)=11.820 | | E(DIHE)=0.000 E(IMPR)=6.161 E(VDW )=5.408 E(ELEC)=4.115 | | E(CDIH)=1.303 E(NOE )=6.758 E(PLAN)=1.936 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=927.801 E(kin)=604.726 temperature=299.667 | | Etotal =323.075 grad(E)=66.393 E(BOND)=210.457 E(ANGL)=334.757 | | E(DIHE)=0.000 E(IMPR)=89.812 E(VDW )=-261.125 E(ELEC)=-135.806 | | E(CDIH)=1.963 E(NOE )=66.695 E(PLAN)=16.322 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=26.261 E(kin)=16.547 temperature=8.200 | | Etotal =21.711 grad(E)=1.597 E(BOND)=11.643 E(ANGL)=13.292 | | E(DIHE)=0.000 E(IMPR)=6.873 E(VDW )=6.429 E(ELEC)=5.698 | | E(CDIH)=1.322 E(NOE )=7.162 E(PLAN)=2.249 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61979 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62078 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62100 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62152 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62191 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62210 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 1.42 A apart NBONDS: found 62248 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 1.44 A apart NBONDS: found 62349 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 1.46 A apart NBONDS: found 62385 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=927.343 E(kin)=606.833 temperature=300.711 | | Etotal =320.510 grad(E)=66.630 E(BOND)=224.945 E(ANGL)=335.532 | | E(DIHE)=0.000 E(IMPR)=79.919 E(VDW )=-253.726 E(ELEC)=-143.472 | | E(CDIH)=3.783 E(NOE )=59.497 E(PLAN)=14.032 | ------------------------------------------------------------------------------- %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 62482 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 62500 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 62471 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 62415 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 62341 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 62295 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62197 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62156 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=931.324 E(kin)=592.075 temperature=293.398 | | Etotal =339.249 grad(E)=69.053 E(BOND)=229.056 E(ANGL)=337.019 | | E(DIHE)=0.000 E(IMPR)=93.223 E(VDW )=-267.912 E(ELEC)=-133.330 | | E(CDIH)=1.998 E(NOE )=64.204 E(PLAN)=14.991 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62165 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62112 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 62132 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62159 intra-atom interactions NBONDS: found 62183 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 62155 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62203 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 62152 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=929.128 E(kin)=604.274 temperature=299.443 | | Etotal =324.854 grad(E)=67.498 E(BOND)=209.910 E(ANGL)=331.195 | | E(DIHE)=0.000 E(IMPR)=92.494 E(VDW )=-267.357 E(ELEC)=-124.923 | | E(CDIH)=1.575 E(NOE )=65.417 E(PLAN)=16.543 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62181 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62218 intra-atom interactions NBONDS: found 62220 intra-atom interactions NBONDS: found 62292 intra-atom interactions NBONDS: found 62330 intra-atom interactions NBONDS: found 62334 intra-atom interactions NBONDS: found 62362 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=912.604 E(kin)=607.171 temperature=300.879 | | Etotal =305.433 grad(E)=67.166 E(BOND)=208.186 E(ANGL)=318.420 | | E(DIHE)=0.000 E(IMPR)=94.809 E(VDW )=-269.911 E(ELEC)=-137.480 | | E(CDIH)=2.076 E(NOE )=70.188 E(PLAN)=19.145 | ------------------------------------------------------------------------------- NBONDS: found 62295 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62236 intra-atom interactions NBONDS: found 62211 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.46 A apart NBONDS: found 62171 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 62068 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 1.49 A apart NBONDS: found 62052 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 62087 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=931.181 E(kin)=635.426 temperature=314.880 | | Etotal =295.755 grad(E)=68.377 E(BOND)=206.706 E(ANGL)=324.774 | | E(DIHE)=0.000 E(IMPR)=89.637 E(VDW )=-258.719 E(ELEC)=-140.024 | | E(CDIH)=0.367 E(NOE )=55.492 E(PLAN)=17.522 | ------------------------------------------------------------------------------- NBONDS: found 62171 intra-atom interactions NBONDS: found 62214 intra-atom interactions NBONDS: found 62238 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62345 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62354 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62384 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart NBONDS: found 62410 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=948.462 E(kin)=607.636 temperature=301.109 | | Etotal =340.826 grad(E)=67.478 E(BOND)=220.898 E(ANGL)=350.359 | | E(DIHE)=0.000 E(IMPR)=82.156 E(VDW )=-274.422 E(ELEC)=-133.290 | | E(CDIH)=1.945 E(NOE )=79.376 E(PLAN)=13.803 | ------------------------------------------------------------------------------- NBONDS: found 62372 intra-atom interactions NBONDS: found 62274 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.49 A apart NBONDS: found 62276 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 1.44 A apart NBONDS: found 62163 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.46 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 62111 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 1.42 A apart NBONDS: found 62022 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=943.220 E(kin)=614.314 temperature=304.419 | | Etotal =328.906 grad(E)=65.610 E(BOND)=221.692 E(ANGL)=313.840 | | E(DIHE)=0.000 E(IMPR)=98.606 E(VDW )=-263.895 E(ELEC)=-130.322 | | E(CDIH)=3.938 E(NOE )=72.149 E(PLAN)=12.898 | ------------------------------------------------------------------------------- %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 62001 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61935 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 61896 intra-atom interactions NBONDS: found 61915 intra-atom interactions NBONDS: found 61964 intra-atom interactions NBONDS: found 61857 intra-atom interactions NBONDS: found 61917 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=920.560 E(kin)=609.849 temperature=302.206 | | Etotal =310.712 grad(E)=65.170 E(BOND)=212.801 E(ANGL)=333.832 | | E(DIHE)=0.000 E(IMPR)=97.579 E(VDW )=-264.437 E(ELEC)=-149.106 | | E(CDIH)=5.453 E(NOE )=58.303 E(PLAN)=16.289 | ------------------------------------------------------------------------------- NBONDS: found 61912 intra-atom interactions NBONDS: found 61954 intra-atom interactions NBONDS: found 62065 intra-atom interactions NBONDS: found 62096 intra-atom interactions NBONDS: found 62039 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=934.559 E(kin)=617.351 temperature=305.924 | | Etotal =317.207 grad(E)=67.410 E(BOND)=226.994 E(ANGL)=316.335 | | E(DIHE)=0.000 E(IMPR)=89.324 E(VDW )=-257.492 E(ELEC)=-136.940 | | E(CDIH)=3.333 E(NOE )=58.657 E(PLAN)=16.997 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62057 intra-atom interactions NBONDS: found 62071 intra-atom interactions NBONDS: found 62131 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62151 intra-atom interactions NBONDS: found 62176 intra-atom interactions NBONDS: found 62151 intra-atom interactions NBONDS: found 62104 intra-atom interactions NBONDS: found 62085 intra-atom interactions NBONDS: found 62048 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=923.508 E(kin)=611.259 temperature=302.904 | | Etotal =312.249 grad(E)=68.867 E(BOND)=217.293 E(ANGL)=341.364 | | E(DIHE)=0.000 E(IMPR)=83.845 E(VDW )=-262.423 E(ELEC)=-137.842 | | E(CDIH)=1.803 E(NOE )=52.395 E(PLAN)=15.814 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=931.707 E(kin)=605.501 temperature=300.051 | | Etotal =326.205 grad(E)=67.767 E(BOND)=216.958 E(ANGL)=336.240 | | E(DIHE)=0.000 E(IMPR)=90.789 E(VDW )=-261.512 E(ELEC)=-136.961 | | E(CDIH)=2.201 E(NOE )=62.966 E(PLAN)=15.524 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.254 E(kin)=12.572 temperature=6.230 | | Etotal =16.494 grad(E)=1.404 E(BOND)=10.392 E(ANGL)=11.095 | | E(DIHE)=0.000 E(IMPR)=6.197 E(VDW )=6.075 E(ELEC)=6.237 | | E(CDIH)=1.471 E(NOE )=6.736 E(PLAN)=2.221 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=928.777 E(kin)=604.920 temperature=299.763 | | Etotal =323.857 grad(E)=66.737 E(BOND)=212.083 E(ANGL)=335.127 | | E(DIHE)=0.000 E(IMPR)=90.056 E(VDW )=-261.222 E(ELEC)=-136.095 | | E(CDIH)=2.022 E(NOE )=65.763 E(PLAN)=16.123 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=23.489 E(kin)=15.652 temperature=7.756 | | Etotal =20.576 grad(E)=1.661 E(BOND)=11.687 E(ANGL)=12.794 | | E(DIHE)=0.000 E(IMPR)=6.724 E(VDW )=6.344 E(ELEC)=5.859 | | E(CDIH)=1.365 E(NOE )=7.240 E(PLAN)=2.268 | ------------------------------------------------------------------------------- NBONDS: found 61992 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart NBONDS: found 61971 intra-atom interactions NBONDS: found 62004 intra-atom interactions NBONDS: found 62014 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62042 intra-atom interactions NBONDS: found 62043 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62058 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62037 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=921.483 E(kin)=593.779 temperature=294.242 | | Etotal =327.704 grad(E)=68.039 E(BOND)=230.594 E(ANGL)=325.714 | | E(DIHE)=0.000 E(IMPR)=94.811 E(VDW )=-257.132 E(ELEC)=-133.796 | | E(CDIH)=1.289 E(NOE )=52.808 E(PLAN)=13.418 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62093 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62120 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62174 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 1.48 A apart NBONDS: found 62178 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 62243 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62272 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62296 intra-atom interactions NBONDS: found 62294 intra-atom interactions NBONDS: found 62300 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=937.110 E(kin)=599.097 temperature=296.878 | | Etotal =338.013 grad(E)=67.143 E(BOND)=233.569 E(ANGL)=332.875 | | E(DIHE)=0.000 E(IMPR)=90.001 E(VDW )=-259.550 E(ELEC)=-136.219 | | E(CDIH)=1.922 E(NOE )=62.691 E(PLAN)=12.725 | ------------------------------------------------------------------------------- NBONDS: found 62241 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62158 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62120 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62098 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62081 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H2' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62022 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62005 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61977 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 62002 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 --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=921.851 E(kin)=576.775 temperature=285.816 | | Etotal =345.076 grad(E)=69.543 E(BOND)=210.413 E(ANGL)=363.096 | | E(DIHE)=0.000 E(IMPR)=89.254 E(VDW )=-257.238 E(ELEC)=-145.529 | | E(CDIH)=1.064 E(NOE )=61.286 E(PLAN)=22.731 | ------------------------------------------------------------------------------- %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 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 61976 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 62016 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 1.45 A apart NBONDS: found 62023 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 1.43 A apart NBONDS: found 61970 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61959 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61868 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61777 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61766 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=928.778 E(kin)=624.961 temperature=309.695 | | Etotal =303.817 grad(E)=65.570 E(BOND)=211.706 E(ANGL)=333.961 | | E(DIHE)=0.000 E(IMPR)=81.920 E(VDW )=-260.951 E(ELEC)=-149.661 | | E(CDIH)=1.186 E(NOE )=67.926 E(PLAN)=17.730 | ------------------------------------------------------------------------------- NBONDS: found 61785 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 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 61797 intra-atom interactions NBONDS: found 61797 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 61817 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 61753 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 61703 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 1.49 A apart NBONDS: found 61670 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=942.814 E(kin)=611.875 temperature=303.210 | | Etotal =330.939 grad(E)=65.615 E(BOND)=214.204 E(ANGL)=341.182 | | E(DIHE)=0.000 E(IMPR)=85.155 E(VDW )=-260.686 E(ELEC)=-135.998 | | E(CDIH)=0.559 E(NOE )=71.886 E(PLAN)=14.638 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 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 61658 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61690 intra-atom interactions NBONDS: found 61763 intra-atom interactions NBONDS: found 61845 intra-atom interactions NBONDS: found 61941 intra-atom interactions NBONDS: found 62024 intra-atom interactions NBONDS: found 62136 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=919.966 E(kin)=604.342 temperature=299.477 | | Etotal =315.624 grad(E)=68.871 E(BOND)=228.221 E(ANGL)=336.710 | | E(DIHE)=0.000 E(IMPR)=79.409 E(VDW )=-272.514 E(ELEC)=-139.846 | | E(CDIH)=2.461 E(NOE )=64.817 E(PLAN)=16.364 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62165 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart NBONDS: found 62286 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.44 A apart NBONDS: found 62291 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart NBONDS: found 62211 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart NBONDS: found 62176 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62151 intra-atom interactions NBONDS: found 62149 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=933.022 E(kin)=612.168 temperature=303.355 | | Etotal =320.853 grad(E)=67.402 E(BOND)=238.633 E(ANGL)=312.098 | | E(DIHE)=0.000 E(IMPR)=88.901 E(VDW )=-261.740 E(ELEC)=-136.410 | | E(CDIH)=2.019 E(NOE )=62.317 E(PLAN)=15.035 | ------------------------------------------------------------------------------- NBONDS: found 62202 intra-atom interactions NBONDS: found 62324 intra-atom interactions NBONDS: found 62542 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62639 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62805 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=936.397 E(kin)=595.218 temperature=294.955 | | Etotal =341.179 grad(E)=69.648 E(BOND)=225.179 E(ANGL)=344.509 | | E(DIHE)=0.000 E(IMPR)=98.732 E(VDW )=-254.069 E(ELEC)=-149.248 | | E(CDIH)=4.359 E(NOE )=50.120 E(PLAN)=21.597 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.39 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62841 intra-atom interactions %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 1.40 A apart NBONDS: found 62836 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.33 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62860 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.31 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62853 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart NBONDS: found 62864 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62812 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62779 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62766 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=933.277 E(kin)=603.324 temperature=298.972 | | Etotal =329.954 grad(E)=68.074 E(BOND)=225.420 E(ANGL)=342.696 | | E(DIHE)=0.000 E(IMPR)=83.668 E(VDW )=-259.939 E(ELEC)=-139.589 | | E(CDIH)=0.689 E(NOE )=59.908 E(PLAN)=17.100 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62708 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62659 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 62649 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62605 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 1.41 A apart NBONDS: found 62547 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 62514 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 62495 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=947.188 E(kin)=624.079 temperature=309.257 | | Etotal =323.109 grad(E)=67.627 E(BOND)=222.693 E(ANGL)=326.997 | | E(DIHE)=0.000 E(IMPR)=90.130 E(VDW )=-247.065 E(ELEC)=-144.895 | | E(CDIH)=1.522 E(NOE )=58.598 E(PLAN)=15.129 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=932.798 E(kin)=605.395 temperature=299.999 | | Etotal =327.403 grad(E)=67.496 E(BOND)=216.307 E(ANGL)=341.292 | | E(DIHE)=0.000 E(IMPR)=89.944 E(VDW )=-259.701 E(ELEC)=-140.774 | | E(CDIH)=1.660 E(NOE )=62.860 E(PLAN)=15.815 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.336 E(kin)=12.295 temperature=6.093 | | Etotal =15.114 grad(E)=1.384 E(BOND)=10.095 E(ANGL)=12.412 | | E(DIHE)=0.000 E(IMPR)=7.012 E(VDW )=5.788 E(ELEC)=5.395 | | E(CDIH)=1.285 E(NOE )=6.108 E(PLAN)=2.101 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=929.581 E(kin)=605.015 temperature=299.810 | | Etotal =324.566 grad(E)=66.889 E(BOND)=212.928 E(ANGL)=336.360 | | E(DIHE)=0.000 E(IMPR)=90.034 E(VDW )=-260.917 E(ELEC)=-137.031 | | E(CDIH)=1.950 E(NOE )=65.182 E(PLAN)=16.061 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=21.480 E(kin)=15.042 temperature=7.454 | | Etotal =19.657 grad(E)=1.638 E(BOND)=11.511 E(ANGL)=12.956 | | E(DIHE)=0.000 E(IMPR)=6.783 E(VDW )=6.267 E(ELEC)=6.065 | | E(CDIH)=1.357 E(NOE )=7.124 E(PLAN)=2.239 | ------------------------------------------------------------------------------- %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 1.46 A apart NBONDS: found 62418 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.33 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62279 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 62177 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62147 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62192 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62127 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=937.290 E(kin)=608.169 temperature=301.373 | | Etotal =329.121 grad(E)=69.396 E(BOND)=206.447 E(ANGL)=350.394 | | E(DIHE)=0.000 E(IMPR)=86.964 E(VDW )=-265.256 E(ELEC)=-146.532 | | E(CDIH)=3.409 E(NOE )=76.785 E(PLAN)=16.910 | ------------------------------------------------------------------------------- NBONDS: found 61977 intra-atom interactions NBONDS: found 61931 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.48 A apart NBONDS: found 61905 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.45 A apart NBONDS: found 61761 intra-atom interactions NBONDS: found 61779 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61809 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=924.070 E(kin)=582.268 temperature=288.538 | | Etotal =341.801 grad(E)=68.644 E(BOND)=210.775 E(ANGL)=364.822 | | E(DIHE)=0.000 E(IMPR)=86.222 E(VDW )=-251.619 E(ELEC)=-136.813 | | E(CDIH)=0.886 E(NOE )=51.670 E(PLAN)=15.859 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61930 intra-atom interactions NBONDS: found 62118 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62179 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.36 A apart NBONDS: found 62146 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=948.083 E(kin)=646.358 temperature=320.297 | | Etotal =301.725 grad(E)=67.013 E(BOND)=218.338 E(ANGL)=334.054 | | E(DIHE)=0.000 E(IMPR)=73.183 E(VDW )=-263.778 E(ELEC)=-134.030 | | E(CDIH)=0.703 E(NOE )=57.940 E(PLAN)=15.316 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62115 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62151 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62177 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62197 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62237 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62231 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62166 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=935.543 E(kin)=596.881 temperature=295.780 | | Etotal =338.662 grad(E)=67.050 E(BOND)=206.077 E(ANGL)=368.598 | | E(DIHE)=0.000 E(IMPR)=86.949 E(VDW )=-261.154 E(ELEC)=-137.557 | | E(CDIH)=3.019 E(NOE )=57.400 E(PLAN)=15.331 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62202 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62135 intra-atom interactions NBONDS: found 62095 intra-atom interactions NBONDS: found 62111 intra-atom interactions NBONDS: found 62068 intra-atom interactions NBONDS: found 62019 intra-atom interactions NBONDS: found 62007 intra-atom interactions NBONDS: found 61962 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=932.256 E(kin)=617.048 temperature=305.773 | | Etotal =315.208 grad(E)=67.125 E(BOND)=208.790 E(ANGL)=347.454 | | E(DIHE)=0.000 E(IMPR)=82.507 E(VDW )=-255.679 E(ELEC)=-134.490 | | E(CDIH)=1.299 E(NOE )=47.004 E(PLAN)=18.324 | ------------------------------------------------------------------------------- NBONDS: found 62002 intra-atom interactions NBONDS: found 62019 intra-atom interactions NBONDS: found 62008 intra-atom interactions NBONDS: found 62087 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 62161 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62157 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=940.231 E(kin)=618.554 temperature=306.520 | | Etotal =321.677 grad(E)=68.332 E(BOND)=211.267 E(ANGL)=352.949 | | E(DIHE)=0.000 E(IMPR)=84.899 E(VDW )=-272.073 E(ELEC)=-145.616 | | E(CDIH)=1.587 E(NOE )=72.315 E(PLAN)=16.349 | ------------------------------------------------------------------------------- %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 62151 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62024 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61870 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61754 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61644 intra-atom interactions NBONDS: found 61527 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=931.218 E(kin)=576.941 temperature=285.898 | | Etotal =354.277 grad(E)=70.713 E(BOND)=219.560 E(ANGL)=374.927 | | E(DIHE)=0.000 E(IMPR)=89.936 E(VDW )=-261.991 E(ELEC)=-141.720 | | E(CDIH)=2.392 E(NOE )=54.109 E(PLAN)=17.065 | ------------------------------------------------------------------------------- NBONDS: found 61559 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61568 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61579 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61575 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61561 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61662 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61696 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 61654 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=931.694 E(kin)=615.578 temperature=305.045 | | Etotal =316.116 grad(E)=67.792 E(BOND)=213.597 E(ANGL)=338.137 | | E(DIHE)=0.000 E(IMPR)=82.403 E(VDW )=-252.697 E(ELEC)=-142.571 | | E(CDIH)=0.373 E(NOE )=63.392 E(PLAN)=13.480 | ------------------------------------------------------------------------------- %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 61651 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61633 intra-atom interactions NBONDS: found 61616 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61636 intra-atom interactions NBONDS: found 61635 intra-atom interactions NBONDS: found 61767 intra-atom interactions NBONDS: found 61780 intra-atom interactions NBONDS: found 61785 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=915.557 E(kin)=603.521 temperature=299.070 | | Etotal =312.036 grad(E)=70.143 E(BOND)=228.169 E(ANGL)=335.462 | | E(DIHE)=0.000 E(IMPR)=85.000 E(VDW )=-264.565 E(ELEC)=-142.557 | | E(CDIH)=0.866 E(NOE )=55.324 E(PLAN)=14.337 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61797 intra-atom interactions NBONDS: found 61817 intra-atom interactions NBONDS: found 61865 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart NBONDS: found 61923 intra-atom interactions NBONDS: found 61914 intra-atom interactions NBONDS: found 61902 intra-atom interactions NBONDS: found 61916 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=929.605 E(kin)=588.358 temperature=291.556 | | Etotal =341.246 grad(E)=68.435 E(BOND)=193.901 E(ANGL)=378.590 | | E(DIHE)=0.000 E(IMPR)=93.091 E(VDW )=-257.463 E(ELEC)=-149.026 | | E(CDIH)=2.278 E(NOE )=59.316 E(PLAN)=20.559 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=932.905 E(kin)=605.536 temperature=300.068 | | Etotal =327.369 grad(E)=68.619 E(BOND)=216.943 E(ANGL)=348.776 | | E(DIHE)=0.000 E(IMPR)=88.192 E(VDW )=-262.572 E(ELEC)=-141.326 | | E(CDIH)=2.006 E(NOE )=60.086 E(PLAN)=15.265 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.377 E(kin)=12.635 temperature=6.261 | | Etotal =15.269 grad(E)=1.433 E(BOND)=9.450 E(ANGL)=11.397 | | E(DIHE)=0.000 E(IMPR)=6.179 E(VDW )=5.143 E(ELEC)=5.092 | | E(CDIH)=1.310 E(NOE )=6.105 E(PLAN)=1.755 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=930.135 E(kin)=605.102 temperature=299.853 | | Etotal =325.033 grad(E)=67.177 E(BOND)=213.597 E(ANGL)=338.430 | | E(DIHE)=0.000 E(IMPR)=89.727 E(VDW )=-261.193 E(ELEC)=-137.747 | | E(CDIH)=1.959 E(NOE )=64.333 E(PLAN)=15.928 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=20.017 E(kin)=14.669 temperature=7.269 | | Etotal =19.025 grad(E)=1.730 E(BOND)=11.294 E(ANGL)=13.525 | | E(DIHE)=0.000 E(IMPR)=6.721 E(VDW )=6.125 E(ELEC)=6.127 | | E(CDIH)=1.349 E(NOE )=7.219 E(PLAN)=2.186 | ------------------------------------------------------------------------------- NBONDS: found 61961 intra-atom interactions NBONDS: found 61991 intra-atom interactions NBONDS: found 62055 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62071 intra-atom interactions NBONDS: found 62043 intra-atom interactions NBONDS: found 62041 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=928.268 E(kin)=628.480 temperature=311.438 | | Etotal =299.788 grad(E)=66.727 E(BOND)=224.358 E(ANGL)=322.518 | | E(DIHE)=0.000 E(IMPR)=95.041 E(VDW )=-264.925 E(ELEC)=-142.879 | | E(CDIH)=0.739 E(NOE )=49.785 E(PLAN)=15.151 | ------------------------------------------------------------------------------- NBONDS: found 62009 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.46 A apart NBONDS: found 62004 intra-atom interactions NBONDS: found 62040 intra-atom interactions NBONDS: found 62096 intra-atom interactions NBONDS: found 62133 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=919.116 E(kin)=601.025 temperature=297.833 | | Etotal =318.092 grad(E)=68.782 E(BOND)=217.285 E(ANGL)=332.972 | | E(DIHE)=0.000 E(IMPR)=94.511 E(VDW )=-258.746 E(ELEC)=-146.368 | | E(CDIH)=0.990 E(NOE )=62.251 E(PLAN)=15.197 | ------------------------------------------------------------------------------- NBONDS: found 62168 intra-atom interactions NBONDS: found 62146 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62056 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61983 intra-atom interactions NBONDS: found 61923 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=930.384 E(kin)=609.869 temperature=302.216 | | Etotal =320.515 grad(E)=68.542 E(BOND)=224.071 E(ANGL)=336.120 | | E(DIHE)=0.000 E(IMPR)=92.322 E(VDW )=-267.911 E(ELEC)=-146.882 | | E(CDIH)=0.557 E(NOE )=66.474 E(PLAN)=15.764 | ------------------------------------------------------------------------------- NBONDS: found 61876 intra-atom interactions NBONDS: found 61909 intra-atom interactions NBONDS: found 61949 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61945 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61954 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61956 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61988 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=931.709 E(kin)=622.174 temperature=308.313 | | Etotal =309.535 grad(E)=68.283 E(BOND)=203.563 E(ANGL)=339.858 | | E(DIHE)=0.000 E(IMPR)=85.082 E(VDW )=-257.416 E(ELEC)=-144.635 | | E(CDIH)=2.853 E(NOE )=63.329 E(PLAN)=16.900 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61966 intra-atom interactions NBONDS: found 61979 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61991 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62037 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 62027 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 1.45 A apart NBONDS: found 61979 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=935.977 E(kin)=594.702 temperature=294.700 | | Etotal =341.275 grad(E)=68.808 E(BOND)=217.989 E(ANGL)=362.233 | | E(DIHE)=0.000 E(IMPR)=87.593 E(VDW )=-266.147 E(ELEC)=-142.177 | | E(CDIH)=0.982 E(NOE )=64.146 E(PLAN)=16.656 | ------------------------------------------------------------------------------- %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 61979 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 61955 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61899 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61819 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 61790 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=930.613 E(kin)=602.286 temperature=298.458 | | Etotal =328.328 grad(E)=67.677 E(BOND)=222.057 E(ANGL)=339.172 | | E(DIHE)=0.000 E(IMPR)=92.660 E(VDW )=-272.234 E(ELEC)=-142.610 | | E(CDIH)=1.641 E(NOE )=72.228 E(PLAN)=15.413 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61741 intra-atom interactions NBONDS: found 61648 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61683 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61676 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61703 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61680 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=927.894 E(kin)=587.712 temperature=291.236 | | Etotal =340.182 grad(E)=71.633 E(BOND)=228.515 E(ANGL)=350.398 | | E(DIHE)=0.000 E(IMPR)=97.364 E(VDW )=-274.063 E(ELEC)=-140.157 | | E(CDIH)=2.073 E(NOE )=65.030 E(PLAN)=11.021 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61679 intra-atom interactions NBONDS: found 61696 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61717 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61772 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61829 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61864 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=920.922 E(kin)=621.759 temperature=308.108 | | Etotal =299.163 grad(E)=69.939 E(BOND)=204.541 E(ANGL)=337.910 | | E(DIHE)=0.000 E(IMPR)=85.035 E(VDW )=-264.084 E(ELEC)=-146.108 | | E(CDIH)=0.427 E(NOE )=64.318 E(PLAN)=17.125 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61889 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61943 intra-atom interactions NBONDS: found 61964 intra-atom interactions NBONDS: found 61955 intra-atom interactions NBONDS: found 62018 intra-atom interactions NBONDS: found 62068 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62099 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62102 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=923.940 E(kin)=628.737 temperature=311.566 | | Etotal =295.203 grad(E)=66.916 E(BOND)=206.979 E(ANGL)=339.971 | | E(DIHE)=0.000 E(IMPR)=77.455 E(VDW )=-260.159 E(ELEC)=-143.674 | | E(CDIH)=1.145 E(NOE )=58.733 E(PLAN)=14.752 | ------------------------------------------------------------------------------- NBONDS: found 62142 intra-atom interactions NBONDS: found 62090 intra-atom interactions NBONDS: found 62136 intra-atom interactions NBONDS: found 62183 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " 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 62113 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62108 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62109 intra-atom interactions NBONDS: found 62067 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=911.176 E(kin)=580.047 temperature=287.438 | | Etotal =331.129 grad(E)=70.534 E(BOND)=227.250 E(ANGL)=339.336 | | E(DIHE)=0.000 E(IMPR)=86.897 E(VDW )=-269.307 E(ELEC)=-140.413 | | E(CDIH)=1.690 E(NOE )=72.369 E(PLAN)=13.308 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.638 E(kin)=605.546 temperature=300.074 | | Etotal =325.092 grad(E)=68.888 E(BOND)=218.721 E(ANGL)=346.344 | | E(DIHE)=0.000 E(IMPR)=89.299 E(VDW )=-262.888 E(ELEC)=-144.203 | | E(CDIH)=1.951 E(NOE )=59.885 E(PLAN)=15.983 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=6.854 E(kin)=12.807 temperature=6.346 | | Etotal =14.031 grad(E)=1.396 E(BOND)=9.633 E(ANGL)=11.516 | | E(DIHE)=0.000 E(IMPR)=6.401 E(VDW )=5.362 E(ELEC)=2.876 | | E(CDIH)=1.354 E(NOE )=5.711 E(PLAN)=2.012 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=930.207 E(kin)=605.165 temperature=299.885 | | Etotal =325.042 grad(E)=67.421 E(BOND)=214.329 E(ANGL)=339.560 | | E(DIHE)=0.000 E(IMPR)=89.666 E(VDW )=-261.435 E(ELEC)=-138.669 | | E(CDIH)=1.958 E(NOE )=63.697 E(PLAN)=15.936 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=18.714 E(kin)=14.419 temperature=7.145 | | Etotal =18.394 grad(E)=1.789 E(BOND)=11.216 E(ANGL)=13.543 | | E(DIHE)=0.000 E(IMPR)=6.678 E(VDW )=6.051 E(ELEC)=6.202 | | E(CDIH)=1.350 E(NOE )=7.194 E(PLAN)=2.162 | ------------------------------------------------------------------------------- NBONDS: found 62062 intra-atom interactions NBONDS: found 62093 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62025 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 1.50 A apart NBONDS: found 62039 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62023 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61993 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61966 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61963 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=932.930 E(kin)=603.530 temperature=299.074 | | Etotal =329.400 grad(E)=67.877 E(BOND)=230.197 E(ANGL)=335.338 | | E(DIHE)=0.000 E(IMPR)=83.382 E(VDW )=-257.598 E(ELEC)=-142.052 | | E(CDIH)=1.188 E(NOE )=63.271 E(PLAN)=15.674 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62002 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62015 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62047 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 62047 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 62009 intra-atom interactions NBONDS: found 62120 intra-atom interactions NBONDS: found 62092 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 62105 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=926.190 E(kin)=598.751 temperature=296.706 | | Etotal =327.439 grad(E)=71.392 E(BOND)=233.473 E(ANGL)=335.444 | | E(DIHE)=0.000 E(IMPR)=92.038 E(VDW )=-270.253 E(ELEC)=-142.411 | | E(CDIH)=0.908 E(NOE )=64.826 E(PLAN)=13.412 | ------------------------------------------------------------------------------- NBONDS: found 62066 intra-atom interactions NBONDS: found 62067 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62032 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 62068 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 62054 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62064 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62100 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62121 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62138 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=935.336 E(kin)=599.229 temperature=296.943 | | Etotal =336.107 grad(E)=70.560 E(BOND)=213.477 E(ANGL)=353.701 | | E(DIHE)=0.000 E(IMPR)=92.182 E(VDW )=-262.189 E(ELEC)=-144.362 | | E(CDIH)=3.009 E(NOE )=65.828 E(PLAN)=14.461 | ------------------------------------------------------------------------------- %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 62159 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62150 intra-atom interactions NBONDS: found 62058 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 1.49 A apart NBONDS: found 62101 intra-atom interactions NBONDS: found 62091 intra-atom interactions NBONDS: found 62073 intra-atom interactions NBONDS: found 62046 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=923.827 E(kin)=604.722 temperature=299.665 | | Etotal =319.105 grad(E)=68.756 E(BOND)=222.291 E(ANGL)=323.302 | | E(DIHE)=0.000 E(IMPR)=91.813 E(VDW )=-263.836 E(ELEC)=-145.358 | | E(CDIH)=2.484 E(NOE )=71.891 E(PLAN)=16.517 | ------------------------------------------------------------------------------- NBONDS: found 62115 intra-atom interactions NBONDS: found 62138 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart NBONDS: found 62188 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.49 A apart NBONDS: found 62257 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62326 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62392 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 1.47 A apart NBONDS: found 62415 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=933.778 E(kin)=599.197 temperature=296.927 | | Etotal =334.581 grad(E)=69.863 E(BOND)=206.303 E(ANGL)=368.088 | | E(DIHE)=0.000 E(IMPR)=96.739 E(VDW )=-262.557 E(ELEC)=-146.153 | | E(CDIH)=0.085 E(NOE )=57.454 E(PLAN)=14.621 | ------------------------------------------------------------------------------- NBONDS: found 62439 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 1.47 A apart NBONDS: found 62519 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 62560 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62586 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62632 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62651 intra-atom interactions %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 62709 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=936.797 E(kin)=613.685 temperature=304.107 | | Etotal =323.111 grad(E)=70.229 E(BOND)=209.184 E(ANGL)=351.926 | | E(DIHE)=0.000 E(IMPR)=93.143 E(VDW )=-260.146 E(ELEC)=-146.120 | | E(CDIH)=2.546 E(NOE )=56.812 E(PLAN)=15.767 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62620 intra-atom interactions NBONDS: found 62633 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 62641 intra-atom interactions NBONDS: found 62618 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 62582 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 62529 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=925.386 E(kin)=600.453 temperature=297.550 | | Etotal =324.933 grad(E)=69.018 E(BOND)=220.362 E(ANGL)=336.108 | | E(DIHE)=0.000 E(IMPR)=96.077 E(VDW )=-254.458 E(ELEC)=-143.496 | | E(CDIH)=0.315 E(NOE )=55.867 E(PLAN)=14.157 | ------------------------------------------------------------------------------- %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 62494 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 62460 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 62399 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62374 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62259 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 62151 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=929.340 E(kin)=612.349 temperature=303.445 | | Etotal =316.991 grad(E)=71.080 E(BOND)=228.094 E(ANGL)=335.793 | | E(DIHE)=0.000 E(IMPR)=83.586 E(VDW )=-271.101 E(ELEC)=-151.612 | | E(CDIH)=2.879 E(NOE )=71.817 E(PLAN)=17.535 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62064 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 61982 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61899 intra-atom interactions NBONDS: found 61877 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61768 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61763 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61729 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 61775 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=928.801 E(kin)=597.527 temperature=296.100 | | Etotal =331.274 grad(E)=68.058 E(BOND)=225.773 E(ANGL)=340.218 | | E(DIHE)=0.000 E(IMPR)=95.560 E(VDW )=-271.056 E(ELEC)=-144.858 | | E(CDIH)=2.155 E(NOE )=66.749 E(PLAN)=16.734 | ------------------------------------------------------------------------------- %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 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61803 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61820 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61787 intra-atom interactions NBONDS: found 61785 intra-atom interactions NBONDS: found 61767 intra-atom interactions NBONDS: found 61680 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=921.891 E(kin)=598.040 temperature=296.354 | | Etotal =323.851 grad(E)=68.577 E(BOND)=226.596 E(ANGL)=335.837 | | E(DIHE)=0.000 E(IMPR)=98.663 E(VDW )=-271.428 E(ELEC)=-145.807 | | E(CDIH)=3.245 E(NOE )=56.904 E(PLAN)=19.841 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=929.640 E(kin)=605.451 temperature=300.027 | | Etotal =324.189 grad(E)=69.499 E(BOND)=218.941 E(ANGL)=341.299 | | E(DIHE)=0.000 E(IMPR)=91.709 E(VDW )=-262.842 E(ELEC)=-143.893 | | E(CDIH)=1.798 E(NOE )=61.106 E(PLAN)=16.072 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.740 E(kin)=12.352 temperature=6.121 | | Etotal =14.148 grad(E)=1.428 E(BOND)=9.608 E(ANGL)=11.289 | | E(DIHE)=0.000 E(IMPR)=6.193 E(VDW )=5.286 E(ELEC)=3.693 | | E(CDIH)=1.363 E(NOE )=6.060 E(PLAN)=2.357 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=930.136 E(kin)=605.201 temperature=299.903 | | Etotal =324.935 grad(E)=67.681 E(BOND)=214.905 E(ANGL)=339.778 | | E(DIHE)=0.000 E(IMPR)=89.921 E(VDW )=-261.611 E(ELEC)=-139.322 | | E(CDIH)=1.938 E(NOE )=63.373 E(PLAN)=15.953 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=17.719 E(kin)=14.177 temperature=7.026 | | Etotal =17.921 grad(E)=1.879 E(BOND)=11.133 E(ANGL)=13.295 | | E(DIHE)=0.000 E(IMPR)=6.654 E(VDW )=5.979 E(ELEC)=6.192 | | E(CDIH)=1.353 E(NOE )=7.114 E(PLAN)=2.188 | ------------------------------------------------------------------------------- NBONDS: found 61747 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61805 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61900 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61925 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61926 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61899 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61890 intra-atom interactions NBONDS: found 61895 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61890 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=925.735 E(kin)=577.343 temperature=286.098 | | Etotal =348.392 grad(E)=71.843 E(BOND)=222.187 E(ANGL)=345.925 | | E(DIHE)=0.000 E(IMPR)=98.056 E(VDW )=-264.133 E(ELEC)=-141.871 | | E(CDIH)=0.946 E(NOE )=70.045 E(PLAN)=17.237 | ------------------------------------------------------------------------------- NBONDS: found 61928 intra-atom interactions NBONDS: found 61950 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61987 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61993 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62050 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62031 intra-atom interactions NBONDS: found 62007 intra-atom interactions NBONDS: found 61951 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=940.929 E(kin)=623.580 temperature=309.010 | | Etotal =317.349 grad(E)=70.609 E(BOND)=219.454 E(ANGL)=335.871 | | E(DIHE)=0.000 E(IMPR)=97.831 E(VDW )=-268.171 E(ELEC)=-143.865 | | E(CDIH)=2.078 E(NOE )=57.208 E(PLAN)=16.943 | ------------------------------------------------------------------------------- NBONDS: found 61928 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61895 intra-atom interactions NBONDS: found 61902 intra-atom interactions NBONDS: found 61849 intra-atom interactions NBONDS: found 61848 intra-atom interactions NBONDS: found 61858 intra-atom interactions NBONDS: found 61846 intra-atom interactions NBONDS: found 61876 intra-atom interactions NBONDS: found 61891 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=927.840 E(kin)=604.124 temperature=299.369 | | Etotal =323.717 grad(E)=69.643 E(BOND)=216.777 E(ANGL)=343.072 | | E(DIHE)=0.000 E(IMPR)=81.521 E(VDW )=-263.881 E(ELEC)=-138.830 | | E(CDIH)=0.990 E(NOE )=65.013 E(PLAN)=19.055 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61970 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61993 intra-atom interactions NBONDS: found 62058 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62112 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62150 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62158 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62157 intra-atom interactions NBONDS: found 62133 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=933.677 E(kin)=616.604 temperature=305.553 | | Etotal =317.073 grad(E)=66.935 E(BOND)=211.220 E(ANGL)=353.278 | | E(DIHE)=0.000 E(IMPR)=77.355 E(VDW )=-257.164 E(ELEC)=-145.026 | | E(CDIH)=1.529 E(NOE )=59.396 E(PLAN)=16.485 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62092 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 1.50 A apart NBONDS: found 62104 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62057 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 62053 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62022 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 62044 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62060 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 62085 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=925.454 E(kin)=608.498 temperature=301.536 | | Etotal =316.956 grad(E)=69.102 E(BOND)=207.753 E(ANGL)=343.596 | | E(DIHE)=0.000 E(IMPR)=105.896 E(VDW )=-260.429 E(ELEC)=-151.172 | | E(CDIH)=0.934 E(NOE )=53.016 E(PLAN)=17.363 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62097 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 62102 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 62011 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62021 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart NBONDS: found 62007 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.45 A apart NBONDS: found 61997 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart NBONDS: found 61985 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=937.380 E(kin)=604.284 temperature=299.448 | | Etotal =333.096 grad(E)=70.077 E(BOND)=220.049 E(ANGL)=337.304 | | E(DIHE)=0.000 E(IMPR)=104.457 E(VDW )=-262.819 E(ELEC)=-138.242 | | E(CDIH)=3.081 E(NOE )=56.564 E(PLAN)=12.702 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart NBONDS: found 61986 intra-atom interactions NBONDS: found 61970 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61931 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61878 intra-atom interactions NBONDS: found 61840 intra-atom interactions NBONDS: found 61775 intra-atom interactions NBONDS: found 61809 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61815 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=917.999 E(kin)=606.268 temperature=300.431 | | Etotal =311.731 grad(E)=67.084 E(BOND)=209.904 E(ANGL)=338.041 | | E(DIHE)=0.000 E(IMPR)=91.519 E(VDW )=-262.533 E(ELEC)=-139.633 | | E(CDIH)=6.565 E(NOE )=49.538 E(PLAN)=18.330 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61790 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61811 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 61761 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 61807 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61785 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61776 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61771 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=925.540 E(kin)=589.931 temperature=292.335 | | Etotal =335.609 grad(E)=71.789 E(BOND)=222.950 E(ANGL)=351.418 | | E(DIHE)=0.000 E(IMPR)=90.319 E(VDW )=-269.180 E(ELEC)=-149.111 | | E(CDIH)=3.089 E(NOE )=67.258 E(PLAN)=18.865 | ------------------------------------------------------------------------------- NBONDS: found 61751 intra-atom interactions NBONDS: found 61695 intra-atom interactions NBONDS: found 61736 intra-atom interactions NBONDS: found 61720 intra-atom interactions NBONDS: found 61633 intra-atom interactions NBONDS: found 61614 intra-atom interactions NBONDS: found 61616 intra-atom interactions NBONDS: found 61621 intra-atom interactions NBONDS: found 61599 intra-atom interactions NBONDS: found 61560 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=928.562 E(kin)=612.397 temperature=303.468 | | Etotal =316.166 grad(E)=67.757 E(BOND)=231.478 E(ANGL)=312.476 | | E(DIHE)=0.000 E(IMPR)=90.015 E(VDW )=-266.265 E(ELEC)=-139.547 | | E(CDIH)=4.023 E(NOE )=65.485 E(PLAN)=18.501 | ------------------------------------------------------------------------------- NBONDS: found 61604 intra-atom interactions NBONDS: found 61628 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61662 intra-atom interactions NBONDS: found 61663 intra-atom interactions NBONDS: found 61670 intra-atom interactions NBONDS: found 61733 intra-atom interactions NBONDS: found 61760 intra-atom interactions NBONDS: found 61738 intra-atom interactions NBONDS: found 61782 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=928.465 E(kin)=586.540 temperature=290.655 | | Etotal =341.926 grad(E)=69.095 E(BOND)=218.067 E(ANGL)=356.360 | | E(DIHE)=0.000 E(IMPR)=98.545 E(VDW )=-260.198 E(ELEC)=-146.603 | | E(CDIH)=2.210 E(NOE )=58.767 E(PLAN)=14.776 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=929.228 E(kin)=605.468 temperature=300.035 | | Etotal =323.760 grad(E)=69.528 E(BOND)=216.248 E(ANGL)=343.955 | | E(DIHE)=0.000 E(IMPR)=91.910 E(VDW )=-264.202 E(ELEC)=-143.145 | | E(CDIH)=2.063 E(NOE )=60.661 E(PLAN)=16.270 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.207 E(kin)=12.863 temperature=6.374 | | Etotal =15.393 grad(E)=1.574 E(BOND)=10.152 E(ANGL)=11.512 | | E(DIHE)=0.000 E(IMPR)=6.609 E(VDW )=4.399 E(ELEC)=3.913 | | E(CDIH)=1.451 E(NOE )=5.709 E(PLAN)=1.882 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=930.035 E(kin)=605.231 temperature=299.917 | | Etotal =324.805 grad(E)=67.886 E(BOND)=215.055 E(ANGL)=340.242 | | E(DIHE)=0.000 E(IMPR)=90.142 E(VDW )=-261.899 E(ELEC)=-139.747 | | E(CDIH)=1.952 E(NOE )=63.072 E(PLAN)=15.988 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=16.987 E(kin)=14.038 temperature=6.956 | | Etotal =17.662 grad(E)=1.936 E(BOND)=11.036 E(ANGL)=13.174 | | E(DIHE)=0.000 E(IMPR)=6.678 E(VDW )=5.881 E(ELEC)=6.101 | | E(CDIH)=1.365 E(NOE )=7.024 E(PLAN)=2.158 | ------------------------------------------------------------------------------- NBONDS: found 61806 intra-atom interactions NBONDS: found 61868 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61925 intra-atom interactions NBONDS: found 61955 intra-atom interactions NBONDS: found 61961 intra-atom interactions NBONDS: found 61984 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61970 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61973 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=934.154 E(kin)=600.003 temperature=297.327 | | Etotal =334.151 grad(E)=69.424 E(BOND)=210.106 E(ANGL)=357.109 | | E(DIHE)=0.000 E(IMPR)=90.827 E(VDW )=-261.878 E(ELEC)=-144.548 | | E(CDIH)=3.077 E(NOE )=65.349 E(PLAN)=14.108 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62039 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 62117 intra-atom interactions %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 1.47 A apart NBONDS: found 62088 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62155 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62178 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 62166 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62147 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62154 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62117 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62024 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=917.617 E(kin)=589.114 temperature=291.931 | | Etotal =328.503 grad(E)=68.945 E(BOND)=206.201 E(ANGL)=354.351 | | E(DIHE)=0.000 E(IMPR)=99.014 E(VDW )=-252.988 E(ELEC)=-145.344 | | E(CDIH)=1.361 E(NOE )=52.562 E(PLAN)=13.347 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61938 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 61899 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61866 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61806 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 61812 intra-atom interactions NBONDS: found 61814 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 61832 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 61844 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=937.674 E(kin)=590.261 temperature=292.499 | | Etotal =347.413 grad(E)=70.779 E(BOND)=215.050 E(ANGL)=361.403 | | E(DIHE)=0.000 E(IMPR)=81.891 E(VDW )=-263.714 E(ELEC)=-142.557 | | E(CDIH)=3.493 E(NOE )=77.229 E(PLAN)=14.618 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61806 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 61852 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 61889 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61956 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 1.49 A apart NBONDS: found 62065 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 61995 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=923.199 E(kin)=602.789 temperature=298.707 | | Etotal =320.410 grad(E)=68.195 E(BOND)=216.509 E(ANGL)=334.773 | | E(DIHE)=0.000 E(IMPR)=91.575 E(VDW )=-260.985 E(ELEC)=-147.689 | | E(CDIH)=2.811 E(NOE )=65.974 E(PLAN)=17.443 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61959 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 61936 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61955 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 62014 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62054 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62092 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62135 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=923.617 E(kin)=616.764 temperature=305.632 | | Etotal =306.853 grad(E)=66.526 E(BOND)=211.744 E(ANGL)=343.413 | | E(DIHE)=0.000 E(IMPR)=86.012 E(VDW )=-256.134 E(ELEC)=-144.680 | | E(CDIH)=2.564 E(NOE )=50.559 E(PLAN)=13.374 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62159 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62145 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62171 intra-atom interactions NBONDS: found 62275 intra-atom interactions NBONDS: found 62323 intra-atom interactions NBONDS: found 62383 intra-atom interactions NBONDS: found 62439 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62484 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62479 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=929.525 E(kin)=600.232 temperature=297.440 | | Etotal =329.293 grad(E)=69.196 E(BOND)=217.481 E(ANGL)=351.038 | | E(DIHE)=0.000 E(IMPR)=96.679 E(VDW )=-267.043 E(ELEC)=-144.830 | | E(CDIH)=2.187 E(NOE )=62.067 E(PLAN)=11.715 | ------------------------------------------------------------------------------- %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 62500 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 62449 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 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62416 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62389 intra-atom interactions NBONDS: found 62333 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.42 A apart NBONDS: found 62269 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 62221 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62210 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62226 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=926.386 E(kin)=631.704 temperature=313.036 | | Etotal =294.681 grad(E)=68.213 E(BOND)=203.378 E(ANGL)=326.646 | | E(DIHE)=0.000 E(IMPR)=82.336 E(VDW )=-261.879 E(ELEC)=-137.387 | | E(CDIH)=0.402 E(NOE )=64.200 E(PLAN)=16.985 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62238 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62273 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62345 intra-atom interactions NBONDS: found 62440 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 62476 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62529 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 62537 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62541 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 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 62517 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=928.434 E(kin)=613.315 temperature=303.923 | | Etotal =315.119 grad(E)=67.033 E(BOND)=210.011 E(ANGL)=343.777 | | E(DIHE)=0.000 E(IMPR)=92.815 E(VDW )=-260.004 E(ELEC)=-145.174 | | E(CDIH)=0.377 E(NOE )=57.136 E(PLAN)=16.181 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62529 intra-atom interactions %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H4' " only 1.49 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62511 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 1.46 A apart NBONDS: found 62490 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 1.49 A apart NBONDS: found 62462 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62409 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 62336 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 1.41 A apart NBONDS: found 62284 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 62266 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 62278 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=939.141 E(kin)=606.249 temperature=300.422 | | Etotal =332.892 grad(E)=67.706 E(BOND)=205.825 E(ANGL)=364.288 | | E(DIHE)=0.000 E(IMPR)=90.673 E(VDW )=-266.553 E(ELEC)=-136.272 | | E(CDIH)=1.057 E(NOE )=55.769 E(PLAN)=18.104 | ------------------------------------------------------------------------------- %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 62226 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 62223 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62284 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 1.50 A apart NBONDS: found 62301 intra-atom interactions NBONDS: found 62257 intra-atom interactions NBONDS: found 62173 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62232 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=928.933 E(kin)=613.647 temperature=304.088 | | Etotal =315.286 grad(E)=68.306 E(BOND)=219.047 E(ANGL)=330.817 | | E(DIHE)=0.000 E(IMPR)=88.824 E(VDW )=-257.652 E(ELEC)=-138.890 | | E(CDIH)=1.602 E(NOE )=51.585 E(PLAN)=19.953 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.928 E(kin)=605.490 temperature=300.046 | | Etotal =325.438 grad(E)=68.500 E(BOND)=216.374 E(ANGL)=345.895 | | E(DIHE)=0.000 E(IMPR)=91.002 E(VDW )=-261.845 E(ELEC)=-142.931 | | E(CDIH)=1.846 E(NOE )=59.341 E(PLAN)=15.757 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.769 E(kin)=12.541 temperature=6.215 | | Etotal =14.297 grad(E)=1.402 E(BOND)=9.309 E(ANGL)=10.897 | | E(DIHE)=0.000 E(IMPR)=6.089 E(VDW )=4.821 E(ELEC)=3.233 | | E(CDIH)=1.418 E(NOE )=6.083 E(PLAN)=1.736 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=930.125 E(kin)=605.257 temperature=299.930 | | Etotal =324.868 grad(E)=67.948 E(BOND)=215.186 E(ANGL)=340.807 | | E(DIHE)=0.000 E(IMPR)=90.228 E(VDW )=-261.894 E(ELEC)=-140.065 | | E(CDIH)=1.941 E(NOE )=62.699 E(PLAN)=15.965 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=16.304 E(kin)=13.896 temperature=6.886 | | Etotal =17.356 grad(E)=1.899 E(BOND)=10.883 E(ANGL)=13.075 | | E(DIHE)=0.000 E(IMPR)=6.627 E(VDW )=5.784 E(ELEC)=5.955 | | E(CDIH)=1.370 E(NOE )=7.025 E(PLAN)=2.121 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62134 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62137 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 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62130 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62069 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62067 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62128 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62148 intra-atom interactions NBONDS: found 62125 intra-atom interactions NBONDS: found 62107 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=932.625 E(kin)=630.051 temperature=312.216 | | Etotal =302.575 grad(E)=66.561 E(BOND)=219.563 E(ANGL)=326.729 | | E(DIHE)=0.000 E(IMPR)=92.611 E(VDW )=-264.376 E(ELEC)=-147.158 | | E(CDIH)=0.914 E(NOE )=59.616 E(PLAN)=14.676 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62101 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62087 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62076 intra-atom interactions NBONDS: found 62025 intra-atom interactions NBONDS: found 62000 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62016 intra-atom interactions NBONDS: found 62017 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=929.494 E(kin)=616.623 temperature=305.562 | | Etotal =312.871 grad(E)=65.620 E(BOND)=198.161 E(ANGL)=334.447 | | E(DIHE)=0.000 E(IMPR)=95.119 E(VDW )=-254.996 E(ELEC)=-136.534 | | E(CDIH)=2.012 E(NOE )=57.931 E(PLAN)=16.731 | ------------------------------------------------------------------------------- NBONDS: found 61966 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61999 intra-atom interactions NBONDS: found 62065 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62137 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62183 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 62211 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62208 intra-atom interactions NBONDS: found 62262 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62249 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=934.614 E(kin)=588.441 temperature=291.597 | | Etotal =346.173 grad(E)=68.370 E(BOND)=226.429 E(ANGL)=344.863 | | E(DIHE)=0.000 E(IMPR)=93.254 E(VDW )=-269.789 E(ELEC)=-138.330 | | E(CDIH)=0.745 E(NOE )=72.950 E(PLAN)=16.050 | ------------------------------------------------------------------------------- NBONDS: found 62268 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 1.45 A apart NBONDS: found 62199 intra-atom interactions NBONDS: found 62145 intra-atom interactions NBONDS: found 62108 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62119 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62067 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 62025 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62037 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=925.490 E(kin)=592.978 temperature=293.846 | | Etotal =332.511 grad(E)=69.113 E(BOND)=225.246 E(ANGL)=340.908 | | E(DIHE)=0.000 E(IMPR)=85.176 E(VDW )=-258.783 E(ELEC)=-137.545 | | E(CDIH)=3.854 E(NOE )=58.231 E(PLAN)=15.424 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61976 intra-atom interactions NBONDS: found 61974 intra-atom interactions NBONDS: found 61945 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61954 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62040 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62091 intra-atom interactions NBONDS: found 62205 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=925.278 E(kin)=592.355 temperature=293.537 | | Etotal =332.923 grad(E)=69.264 E(BOND)=238.384 E(ANGL)=336.035 | | E(DIHE)=0.000 E(IMPR)=95.376 E(VDW )=-261.006 E(ELEC)=-143.966 | | E(CDIH)=1.525 E(NOE )=49.546 E(PLAN)=17.029 | ------------------------------------------------------------------------------- NBONDS: found 62302 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart NBONDS: found 62314 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.48 A apart NBONDS: found 62374 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 62337 intra-atom interactions NBONDS: found 62288 intra-atom interactions NBONDS: found 62285 intra-atom interactions NBONDS: found 62274 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62281 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 1.45 A apart NBONDS: found 62259 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=937.918 E(kin)=598.738 temperature=296.700 | | Etotal =339.179 grad(E)=69.330 E(BOND)=213.288 E(ANGL)=351.915 | | E(DIHE)=0.000 E(IMPR)=94.973 E(VDW )=-260.045 E(ELEC)=-137.392 | | E(CDIH)=0.115 E(NOE )=58.071 E(PLAN)=18.256 | ------------------------------------------------------------------------------- %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 62300 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62266 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 62259 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 62310 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62240 intra-atom interactions NBONDS: found 62255 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 62186 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=939.412 E(kin)=593.846 temperature=294.275 | | Etotal =345.567 grad(E)=71.019 E(BOND)=219.945 E(ANGL)=344.272 | | E(DIHE)=0.000 E(IMPR)=107.646 E(VDW )=-265.933 E(ELEC)=-135.961 | | E(CDIH)=0.539 E(NOE )=58.643 E(PLAN)=16.416 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 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 62082 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62075 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 1.45 A apart NBONDS: found 62049 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 62016 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61940 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 61957 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61946 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=925.433 E(kin)=611.901 temperature=303.223 | | Etotal =313.532 grad(E)=67.231 E(BOND)=213.739 E(ANGL)=334.684 | | E(DIHE)=0.000 E(IMPR)=89.937 E(VDW )=-261.704 E(ELEC)=-142.361 | | E(CDIH)=0.447 E(NOE )=63.103 E(PLAN)=15.687 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61925 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 1.45 A apart NBONDS: found 61896 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61849 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61792 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.46 A apart NBONDS: found 61742 intra-atom interactions NBONDS: found 61727 intra-atom interactions NBONDS: found 61707 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61693 intra-atom interactions NBONDS: found 61637 intra-atom interactions NBONDS: found 61682 intra-atom interactions NBONDS: found 61669 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=936.399 E(kin)=595.522 temperature=295.106 | | Etotal =340.877 grad(E)=68.967 E(BOND)=232.406 E(ANGL)=347.929 | | E(DIHE)=0.000 E(IMPR)=90.321 E(VDW )=-268.284 E(ELEC)=-140.167 | | E(CDIH)=1.463 E(NOE )=57.888 E(PLAN)=19.321 | ------------------------------------------------------------------------------- NBONDS: found 61785 intra-atom interactions NBONDS: found 61882 intra-atom interactions NBONDS: found 61936 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62045 intra-atom interactions NBONDS: found 62125 intra-atom interactions NBONDS: found 62183 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=933.207 E(kin)=585.990 temperature=290.383 | | Etotal =347.216 grad(E)=69.916 E(BOND)=246.163 E(ANGL)=340.147 | | E(DIHE)=0.000 E(IMPR)=88.370 E(VDW )=-256.032 E(ELEC)=-140.926 | | E(CDIH)=1.861 E(NOE )=50.871 E(PLAN)=16.763 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=931.835 E(kin)=605.460 temperature=300.031 | | Etotal =326.375 grad(E)=68.275 E(BOND)=217.749 E(ANGL)=342.641 | | E(DIHE)=0.000 E(IMPR)=91.683 E(VDW )=-262.370 E(ELEC)=-140.524 | | E(CDIH)=1.882 E(NOE )=59.517 E(PLAN)=15.798 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.108 E(kin)=12.515 temperature=6.202 | | Etotal =15.056 grad(E)=1.406 E(BOND)=9.434 E(ANGL)=11.583 | | E(DIHE)=0.000 E(IMPR)=6.390 E(VDW )=4.819 E(ELEC)=4.909 | | E(CDIH)=1.189 E(NOE )=6.059 E(PLAN)=2.051 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=930.280 E(kin)=605.275 temperature=299.939 | | Etotal =325.005 grad(E)=67.977 E(BOND)=215.419 E(ANGL)=340.974 | | E(DIHE)=0.000 E(IMPR)=90.360 E(VDW )=-261.937 E(ELEC)=-140.107 | | E(CDIH)=1.936 E(NOE )=62.410 E(PLAN)=15.950 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=15.793 E(kin)=13.776 temperature=6.827 | | Etotal =17.165 grad(E)=1.862 E(BOND)=10.785 E(ANGL)=12.957 | | E(DIHE)=0.000 E(IMPR)=6.619 E(VDW )=5.704 E(ELEC)=5.869 | | E(CDIH)=1.355 E(NOE )=7.003 E(PLAN)=2.115 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62242 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62219 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62188 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62102 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62077 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62025 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61996 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61950 intra-atom interactions NBONDS: found 61909 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=945.460 E(kin)=605.640 temperature=300.120 | | Etotal =339.820 grad(E)=70.429 E(BOND)=227.748 E(ANGL)=351.231 | | E(DIHE)=0.000 E(IMPR)=92.122 E(VDW )=-269.849 E(ELEC)=-139.654 | | E(CDIH)=0.480 E(NOE )=65.094 E(PLAN)=12.648 | ------------------------------------------------------------------------------- NBONDS: found 61954 intra-atom interactions NBONDS: found 62005 intra-atom interactions NBONDS: found 61997 intra-atom interactions NBONDS: found 62017 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62071 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62131 intra-atom interactions NBONDS: found 62137 intra-atom interactions NBONDS: found 62110 intra-atom interactions NBONDS: found 62104 intra-atom interactions NBONDS: found 62142 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=929.269 E(kin)=592.222 temperature=293.471 | | Etotal =337.047 grad(E)=68.468 E(BOND)=214.045 E(ANGL)=354.688 | | E(DIHE)=0.000 E(IMPR)=91.813 E(VDW )=-258.344 E(ELEC)=-141.790 | | E(CDIH)=2.671 E(NOE )=60.104 E(PLAN)=13.860 | ------------------------------------------------------------------------------- NBONDS: found 62144 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62082 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62066 intra-atom interactions NBONDS: found 62067 intra-atom interactions NBONDS: found 62029 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 62016 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=936.239 E(kin)=582.272 temperature=288.540 | | Etotal =353.967 grad(E)=71.711 E(BOND)=228.571 E(ANGL)=340.189 | | E(DIHE)=0.000 E(IMPR)=108.367 E(VDW )=-263.094 E(ELEC)=-142.131 | | E(CDIH)=1.350 E(NOE )=63.564 E(PLAN)=17.152 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62035 intra-atom interactions NBONDS: found 62100 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H5' " only 1.42 A apart NBONDS: found 62128 intra-atom interactions NBONDS: found 62180 intra-atom interactions NBONDS: found 62294 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 62396 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 62472 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62489 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=926.415 E(kin)=575.316 temperature=285.093 | | Etotal =351.099 grad(E)=70.437 E(BOND)=235.611 E(ANGL)=354.572 | | E(DIHE)=0.000 E(IMPR)=89.457 E(VDW )=-256.028 E(ELEC)=-148.283 | | E(CDIH)=1.433 E(NOE )=58.104 E(PLAN)=16.233 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62465 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62401 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 62384 intra-atom interactions NBONDS: found 62298 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62282 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 62160 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=914.755 E(kin)=606.642 temperature=300.616 | | Etotal =308.114 grad(E)=67.947 E(BOND)=210.662 E(ANGL)=342.273 | | E(DIHE)=0.000 E(IMPR)=87.994 E(VDW )=-267.435 E(ELEC)=-149.482 | | E(CDIH)=2.101 E(NOE )=69.860 E(PLAN)=12.141 | ------------------------------------------------------------------------------- %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 62093 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62061 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61981 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61972 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 61970 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61976 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=933.182 E(kin)=621.087 temperature=307.775 | | Etotal =312.095 grad(E)=68.949 E(BOND)=220.179 E(ANGL)=327.671 | | E(DIHE)=0.000 E(IMPR)=98.146 E(VDW )=-265.638 E(ELEC)=-145.093 | | E(CDIH)=2.920 E(NOE )=60.573 E(PLAN)=13.336 | ------------------------------------------------------------------------------- NBONDS: found 61982 intra-atom interactions NBONDS: found 62057 intra-atom interactions NBONDS: found 61990 intra-atom interactions NBONDS: found 61923 intra-atom interactions NBONDS: found 61875 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61802 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61753 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61689 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=922.478 E(kin)=604.994 temperature=299.800 | | Etotal =317.484 grad(E)=67.387 E(BOND)=224.346 E(ANGL)=346.475 | | E(DIHE)=0.000 E(IMPR)=84.282 E(VDW )=-267.256 E(ELEC)=-146.342 | | E(CDIH)=0.327 E(NOE )=60.544 E(PLAN)=15.110 | ------------------------------------------------------------------------------- NBONDS: found 61666 intra-atom interactions NBONDS: found 61641 intra-atom interactions NBONDS: found 61569 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61685 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61693 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61736 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=941.416 E(kin)=609.249 temperature=301.908 | | Etotal =332.167 grad(E)=67.757 E(BOND)=225.094 E(ANGL)=350.566 | | E(DIHE)=0.000 E(IMPR)=102.552 E(VDW )=-258.820 E(ELEC)=-149.708 | | E(CDIH)=0.913 E(NOE )=47.808 E(PLAN)=13.761 | ------------------------------------------------------------------------------- NBONDS: found 61813 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61867 intra-atom interactions NBONDS: found 61827 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61772 intra-atom interactions NBONDS: found 61774 intra-atom interactions NBONDS: found 61753 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=917.646 E(kin)=603.371 temperature=298.996 | | Etotal =314.275 grad(E)=70.726 E(BOND)=222.366 E(ANGL)=318.202 | | E(DIHE)=0.000 E(IMPR)=96.245 E(VDW )=-255.643 E(ELEC)=-142.051 | | E(CDIH)=1.206 E(NOE )=56.432 E(PLAN)=17.519 | ------------------------------------------------------------------------------- NBONDS: found 61745 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61721 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61756 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61631 intra-atom interactions NBONDS: found 61556 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=928.366 E(kin)=610.337 temperature=302.447 | | Etotal =318.029 grad(E)=67.863 E(BOND)=217.211 E(ANGL)=334.111 | | E(DIHE)=0.000 E(IMPR)=89.342 E(VDW )=-267.254 E(ELEC)=-137.610 | | E(CDIH)=4.207 E(NOE )=61.919 E(PLAN)=16.103 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.099 E(kin)=605.520 temperature=300.061 | | Etotal =324.579 grad(E)=68.517 E(BOND)=219.974 E(ANGL)=342.070 | | E(DIHE)=0.000 E(IMPR)=93.268 E(VDW )=-262.890 E(ELEC)=-144.610 | | E(CDIH)=1.814 E(NOE )=59.430 E(PLAN)=15.523 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.290 E(kin)=12.970 temperature=6.427 | | Etotal =15.496 grad(E)=1.478 E(BOND)=9.950 E(ANGL)=12.679 | | E(DIHE)=0.000 E(IMPR)=6.510 E(VDW )=5.354 E(ELEC)=4.368 | | E(CDIH)=1.251 E(NOE )=6.043 E(PLAN)=1.621 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=930.265 E(kin)=605.296 temperature=299.949 | | Etotal =324.969 grad(E)=68.022 E(BOND)=215.799 E(ANGL)=341.065 | | E(DIHE)=0.000 E(IMPR)=90.603 E(VDW )=-262.016 E(ELEC)=-140.482 | | E(CDIH)=1.926 E(NOE )=62.161 E(PLAN)=15.914 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=15.357 E(kin)=13.711 temperature=6.794 | | Etotal =17.032 grad(E)=1.839 E(BOND)=10.791 E(ANGL)=12.938 | | E(DIHE)=0.000 E(IMPR)=6.658 E(VDW )=5.682 E(ELEC)=5.892 | | E(CDIH)=1.347 E(NOE )=6.977 E(PLAN)=2.082 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61562 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61608 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 61675 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 61737 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61784 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61849 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61929 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61906 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=930.241 E(kin)=640.471 temperature=317.380 | | Etotal =289.771 grad(E)=66.129 E(BOND)=214.779 E(ANGL)=326.026 | | E(DIHE)=0.000 E(IMPR)=88.879 E(VDW )=-264.565 E(ELEC)=-149.712 | | E(CDIH)=1.398 E(NOE )=59.208 E(PLAN)=13.758 | ------------------------------------------------------------------------------- %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 61951 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 1.45 A apart NBONDS: found 61880 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 1.46 A apart NBONDS: found 61870 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 1.39 A apart NBONDS: found 61863 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 61816 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 61820 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=940.819 E(kin)=595.125 temperature=294.909 | | Etotal =345.694 grad(E)=67.236 E(BOND)=234.320 E(ANGL)=353.793 | | E(DIHE)=0.000 E(IMPR)=88.402 E(VDW )=-258.331 E(ELEC)=-144.984 | | E(CDIH)=1.195 E(NOE )=56.474 E(PLAN)=14.825 | ------------------------------------------------------------------------------- %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 61854 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 61883 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 61892 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61886 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 61956 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.40 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 1.46 A apart NBONDS: found 62033 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 62077 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=927.569 E(kin)=607.707 temperature=301.144 | | Etotal =319.862 grad(E)=67.133 E(BOND)=213.011 E(ANGL)=357.119 | | E(DIHE)=0.000 E(IMPR)=78.650 E(VDW )=-264.392 E(ELEC)=-141.303 | | E(CDIH)=1.024 E(NOE )=61.586 E(PLAN)=14.167 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62073 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 62085 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62034 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 62050 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 62121 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62126 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=937.258 E(kin)=596.316 temperature=295.499 | | Etotal =340.942 grad(E)=67.975 E(BOND)=220.914 E(ANGL)=346.164 | | E(DIHE)=0.000 E(IMPR)=94.711 E(VDW )=-254.589 E(ELEC)=-149.607 | | E(CDIH)=2.643 E(NOE )=63.049 E(PLAN)=17.657 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62083 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62061 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 1.47 A apart NBONDS: found 62078 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 62043 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.47 A apart NBONDS: found 62025 intra-atom interactions NBONDS: found 61987 intra-atom interactions NBONDS: found 61948 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=929.877 E(kin)=619.008 temperature=306.744 | | Etotal =310.869 grad(E)=68.794 E(BOND)=206.791 E(ANGL)=345.586 | | E(DIHE)=0.000 E(IMPR)=87.444 E(VDW )=-268.594 E(ELEC)=-136.102 | | E(CDIH)=4.722 E(NOE )=53.831 E(PLAN)=17.191 | ------------------------------------------------------------------------------- NBONDS: found 61944 intra-atom interactions NBONDS: found 61925 intra-atom interactions NBONDS: found 61921 intra-atom interactions NBONDS: found 61987 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 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 62081 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62115 intra-atom interactions NBONDS: found 62114 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=926.155 E(kin)=615.310 temperature=304.912 | | Etotal =310.844 grad(E)=69.323 E(BOND)=215.944 E(ANGL)=354.973 | | E(DIHE)=0.000 E(IMPR)=78.999 E(VDW )=-265.477 E(ELEC)=-147.417 | | E(CDIH)=0.516 E(NOE )=57.128 E(PLAN)=16.177 | ------------------------------------------------------------------------------- NBONDS: found 62121 intra-atom interactions NBONDS: found 62130 intra-atom interactions NBONDS: found 62052 intra-atom interactions NBONDS: found 62027 intra-atom interactions NBONDS: found 62036 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=930.226 E(kin)=617.790 temperature=306.141 | | Etotal =312.436 grad(E)=68.522 E(BOND)=223.778 E(ANGL)=337.358 | | E(DIHE)=0.000 E(IMPR)=89.350 E(VDW )=-267.522 E(ELEC)=-146.710 | | E(CDIH)=0.075 E(NOE )=60.671 E(PLAN)=15.436 | ------------------------------------------------------------------------------- NBONDS: found 62108 intra-atom interactions NBONDS: found 62190 intra-atom interactions NBONDS: found 62160 intra-atom interactions NBONDS: found 62214 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62125 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62091 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62062 intra-atom interactions NBONDS: found 62053 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=924.591 E(kin)=623.967 temperature=309.202 | | Etotal =300.624 grad(E)=69.534 E(BOND)=223.487 E(ANGL)=327.530 | | E(DIHE)=0.000 E(IMPR)=94.564 E(VDW )=-269.570 E(ELEC)=-149.018 | | E(CDIH)=2.442 E(NOE )=57.929 E(PLAN)=13.259 | ------------------------------------------------------------------------------- NBONDS: found 62043 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62087 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 62121 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62117 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62117 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 62106 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 1.44 A apart NBONDS: found 62061 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 62049 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=928.919 E(kin)=631.144 temperature=312.758 | | Etotal =297.775 grad(E)=66.748 E(BOND)=214.908 E(ANGL)=325.869 | | E(DIHE)=0.000 E(IMPR)=100.325 E(VDW )=-269.369 E(ELEC)=-147.196 | | E(CDIH)=0.903 E(NOE )=54.975 E(PLAN)=17.360 | ------------------------------------------------------------------------------- %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 62119 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 62128 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62175 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62205 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 62174 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 62090 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62064 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=926.783 E(kin)=610.522 temperature=302.539 | | Etotal =316.261 grad(E)=67.124 E(BOND)=208.064 E(ANGL)=333.494 | | E(DIHE)=0.000 E(IMPR)=97.013 E(VDW )=-262.551 E(ELEC)=-143.367 | | E(CDIH)=2.362 E(NOE )=65.307 E(PLAN)=15.940 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.508 E(kin)=605.483 temperature=300.042 | | Etotal =325.025 grad(E)=68.130 E(BOND)=219.978 E(ANGL)=344.801 | | E(DIHE)=0.000 E(IMPR)=91.628 E(VDW )=-264.144 E(ELEC)=-145.101 | | E(CDIH)=1.989 E(NOE )=60.111 E(PLAN)=15.764 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.765 E(kin)=12.555 temperature=6.221 | | Etotal =14.813 grad(E)=1.446 E(BOND)=9.837 E(ANGL)=11.201 | | E(DIHE)=0.000 E(IMPR)=6.607 E(VDW )=4.715 E(ELEC)=4.117 | | E(CDIH)=1.360 E(NOE )=5.900 E(PLAN)=1.874 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=930.284 E(kin)=605.310 temperature=299.957 | | Etotal =324.974 grad(E)=68.031 E(BOND)=216.120 E(ANGL)=341.353 | | E(DIHE)=0.000 E(IMPR)=90.681 E(VDW )=-262.180 E(ELEC)=-140.837 | | E(CDIH)=1.931 E(NOE )=62.004 E(PLAN)=15.903 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=14.954 E(kin)=13.625 temperature=6.752 | | Etotal =16.872 grad(E)=1.812 E(BOND)=10.778 E(ANGL)=12.851 | | E(DIHE)=0.000 E(IMPR)=6.660 E(VDW )=5.642 E(ELEC)=5.904 | | E(CDIH)=1.348 E(NOE )=6.921 E(PLAN)=2.067 | ------------------------------------------------------------------------------- NBONDS: found 62045 intra-atom interactions NBONDS: found 62012 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 61865 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61907 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 1.49 A apart NBONDS: found 61853 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61799 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.49 A apart NBONDS: found 61740 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.50 A apart %atoms "A -11 -ADE -HO2'" and "A -12 -URI -H5' " only 1.48 A apart NBONDS: found 61654 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=928.698 E(kin)=628.955 temperature=311.674 | | Etotal =299.744 grad(E)=66.417 E(BOND)=219.023 E(ANGL)=311.238 | | E(DIHE)=0.000 E(IMPR)=100.693 E(VDW )=-262.129 E(ELEC)=-145.868 | | E(CDIH)=3.078 E(NOE )=57.489 E(PLAN)=16.220 | ------------------------------------------------------------------------------- %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 1.46 A apart NBONDS: found 61571 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61498 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61452 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 61524 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 61533 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61615 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61748 intra-atom interactions NBONDS: found 61815 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=911.287 E(kin)=592.572 temperature=293.644 | | Etotal =318.715 grad(E)=69.652 E(BOND)=234.458 E(ANGL)=339.906 | | E(DIHE)=0.000 E(IMPR)=85.903 E(VDW )=-264.202 E(ELEC)=-145.266 | | E(CDIH)=1.325 E(NOE )=52.534 E(PLAN)=14.058 | ------------------------------------------------------------------------------- NBONDS: found 61851 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61941 intra-atom interactions NBONDS: found 61868 intra-atom interactions NBONDS: found 61850 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 61805 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61781 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61740 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61682 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=935.309 E(kin)=609.688 temperature=302.126 | | Etotal =325.621 grad(E)=69.427 E(BOND)=228.158 E(ANGL)=342.085 | | E(DIHE)=0.000 E(IMPR)=83.306 E(VDW )=-263.105 E(ELEC)=-141.082 | | E(CDIH)=2.205 E(NOE )=62.024 E(PLAN)=12.030 | ------------------------------------------------------------------------------- NBONDS: found 61662 intra-atom interactions NBONDS: found 61646 intra-atom interactions NBONDS: found 61753 intra-atom interactions NBONDS: found 61841 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61920 intra-atom interactions NBONDS: found 61982 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=944.732 E(kin)=603.882 temperature=299.249 | | Etotal =340.850 grad(E)=69.265 E(BOND)=234.588 E(ANGL)=328.753 | | E(DIHE)=0.000 E(IMPR)=96.404 E(VDW )=-258.461 E(ELEC)=-144.969 | | E(CDIH)=0.752 E(NOE )=67.032 E(PLAN)=16.752 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62069 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62117 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 62146 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62173 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62212 intra-atom interactions NBONDS: found 62189 intra-atom interactions NBONDS: found 62132 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=919.698 E(kin)=591.157 temperature=292.943 | | Etotal =328.541 grad(E)=72.543 E(BOND)=231.843 E(ANGL)=331.802 | | E(DIHE)=0.000 E(IMPR)=104.207 E(VDW )=-266.955 E(ELEC)=-147.007 | | E(CDIH)=2.265 E(NOE )=57.177 E(PLAN)=15.208 | ------------------------------------------------------------------------------- NBONDS: found 62014 intra-atom interactions NBONDS: found 62018 intra-atom interactions NBONDS: found 61972 intra-atom interactions NBONDS: found 61962 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.45 A apart NBONDS: found 61947 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.48 A apart NBONDS: found 61908 intra-atom interactions NBONDS: found 61883 intra-atom interactions NBONDS: found 61907 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=936.983 E(kin)=607.543 temperature=301.063 | | Etotal =329.440 grad(E)=69.693 E(BOND)=223.875 E(ANGL)=343.291 | | E(DIHE)=0.000 E(IMPR)=91.834 E(VDW )=-273.158 E(ELEC)=-134.095 | | E(CDIH)=0.652 E(NOE )=63.162 E(PLAN)=13.879 | ------------------------------------------------------------------------------- NBONDS: found 61997 intra-atom interactions NBONDS: found 62065 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 62125 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 62216 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 62241 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 62259 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=939.281 E(kin)=619.953 temperature=307.213 | | Etotal =319.328 grad(E)=70.949 E(BOND)=207.600 E(ANGL)=335.381 | | E(DIHE)=0.000 E(IMPR)=104.666 E(VDW )=-263.056 E(ELEC)=-147.674 | | E(CDIH)=0.653 E(NOE )=65.546 E(PLAN)=16.211 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62268 intra-atom interactions NBONDS: found 62240 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62209 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62128 intra-atom interactions NBONDS: found 62102 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62074 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=926.612 E(kin)=599.456 temperature=297.056 | | Etotal =327.156 grad(E)=71.433 E(BOND)=230.627 E(ANGL)=323.804 | | E(DIHE)=0.000 E(IMPR)=104.632 E(VDW )=-264.860 E(ELEC)=-141.346 | | E(CDIH)=2.355 E(NOE )=54.496 E(PLAN)=17.448 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62098 intra-atom interactions NBONDS: found 62179 intra-atom interactions NBONDS: found 62164 intra-atom interactions NBONDS: found 62123 intra-atom interactions NBONDS: found 62126 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62068 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 62007 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 1.41 A apart NBONDS: found 62011 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=945.425 E(kin)=598.095 temperature=296.381 | | Etotal =347.330 grad(E)=70.596 E(BOND)=226.685 E(ANGL)=360.901 | | E(DIHE)=0.000 E(IMPR)=88.721 E(VDW )=-260.369 E(ELEC)=-137.203 | | E(CDIH)=3.313 E(NOE )=49.844 E(PLAN)=15.438 | ------------------------------------------------------------------------------- %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 61925 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 61851 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61919 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 1.41 A apart NBONDS: found 61950 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62002 intra-atom interactions NBONDS: found 62059 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=928.667 E(kin)=584.379 temperature=289.584 | | Etotal =344.287 grad(E)=72.733 E(BOND)=231.040 E(ANGL)=352.011 | | E(DIHE)=0.000 E(IMPR)=85.604 E(VDW )=-263.659 E(ELEC)=-144.407 | | E(CDIH)=2.387 E(NOE )=68.150 E(PLAN)=13.162 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=932.519 E(kin)=605.494 temperature=300.048 | | Etotal =327.025 grad(E)=69.337 E(BOND)=223.327 E(ANGL)=341.376 | | E(DIHE)=0.000 E(IMPR)=93.296 E(VDW )=-263.335 E(ELEC)=-143.343 | | E(CDIH)=1.965 E(NOE )=58.138 E(PLAN)=15.601 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.745 E(kin)=12.861 temperature=6.373 | | Etotal =14.629 grad(E)=1.509 E(BOND)=10.270 E(ANGL)=11.414 | | E(DIHE)=0.000 E(IMPR)=6.555 E(VDW )=4.883 E(ELEC)=4.005 | | E(CDIH)=1.386 E(NOE )=5.791 E(PLAN)=1.759 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=930.443 E(kin)=605.323 temperature=299.963 | | Etotal =325.120 grad(E)=68.124 E(BOND)=216.635 E(ANGL)=341.354 | | E(DIHE)=0.000 E(IMPR)=90.868 E(VDW )=-262.262 E(ELEC)=-141.016 | | E(CDIH)=1.933 E(NOE )=61.727 E(PLAN)=15.881 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=14.569 E(kin)=13.572 temperature=6.726 | | Etotal =16.730 grad(E)=1.823 E(BOND)=10.902 E(ANGL)=12.754 | | E(DIHE)=0.000 E(IMPR)=6.687 E(VDW )=5.599 E(ELEC)=5.825 | | E(CDIH)=1.351 E(NOE )=6.919 E(PLAN)=2.048 | ------------------------------------------------------------------------------- NBONDS: found 62169 intra-atom interactions NBONDS: found 62133 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62135 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62085 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62150 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62184 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62184 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=940.403 E(kin)=614.652 temperature=304.586 | | Etotal =325.751 grad(E)=68.378 E(BOND)=213.060 E(ANGL)=351.903 | | E(DIHE)=0.000 E(IMPR)=88.832 E(VDW )=-259.825 E(ELEC)=-142.350 | | E(CDIH)=1.918 E(NOE )=57.239 E(PLAN)=14.974 | ------------------------------------------------------------------------------- NBONDS: found 62226 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62223 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62233 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 1.40 A apart NBONDS: found 62271 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 62230 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 62207 intra-atom interactions NBONDS: found 62152 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=940.879 E(kin)=605.137 temperature=299.871 | | Etotal =335.742 grad(E)=66.653 E(BOND)=225.449 E(ANGL)=361.315 | | E(DIHE)=0.000 E(IMPR)=95.509 E(VDW )=-270.254 E(ELEC)=-140.368 | | E(CDIH)=0.379 E(NOE )=50.291 E(PLAN)=13.420 | ------------------------------------------------------------------------------- NBONDS: found 62057 intra-atom interactions NBONDS: found 62010 intra-atom interactions NBONDS: found 61966 intra-atom interactions NBONDS: found 61964 intra-atom interactions NBONDS: found 61960 intra-atom interactions NBONDS: found 61949 intra-atom interactions NBONDS: found 61937 intra-atom interactions NBONDS: found 61913 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=934.754 E(kin)=611.761 temperature=303.153 | | Etotal =322.993 grad(E)=68.163 E(BOND)=234.190 E(ANGL)=342.853 | | E(DIHE)=0.000 E(IMPR)=85.409 E(VDW )=-265.220 E(ELEC)=-147.090 | | E(CDIH)=1.217 E(NOE )=55.223 E(PLAN)=16.412 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61842 intra-atom interactions NBONDS: found 61777 intra-atom interactions NBONDS: found 61713 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61637 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 1.49 A apart NBONDS: found 61614 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61637 intra-atom interactions NBONDS: found 61759 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=929.380 E(kin)=589.180 temperature=291.963 | | Etotal =340.201 grad(E)=70.773 E(BOND)=224.463 E(ANGL)=368.739 | | E(DIHE)=0.000 E(IMPR)=85.007 E(VDW )=-262.401 E(ELEC)=-148.583 | | E(CDIH)=0.258 E(NOE )=55.481 E(PLAN)=17.237 | ------------------------------------------------------------------------------- NBONDS: found 61742 intra-atom interactions NBONDS: found 61762 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61831 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61925 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 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 62043 intra-atom interactions NBONDS: found 62043 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart NBONDS: found 62038 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=949.790 E(kin)=626.480 temperature=310.447 | | Etotal =323.309 grad(E)=69.439 E(BOND)=229.713 E(ANGL)=344.307 | | E(DIHE)=0.000 E(IMPR)=87.550 E(VDW )=-268.487 E(ELEC)=-151.887 | | E(CDIH)=0.381 E(NOE )=63.733 E(PLAN)=18.001 | ------------------------------------------------------------------------------- NBONDS: found 62033 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 61925 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61849 intra-atom interactions NBONDS: found 61821 intra-atom interactions NBONDS: found 61851 intra-atom interactions %atoms "A -11 -ADE -H2' " and "A -12 -URI -O4' " only 1.46 A apart NBONDS: found 61833 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61825 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=925.088 E(kin)=618.901 temperature=306.691 | | Etotal =306.188 grad(E)=68.724 E(BOND)=205.371 E(ANGL)=343.528 | | E(DIHE)=0.000 E(IMPR)=86.169 E(VDW )=-263.813 E(ELEC)=-142.033 | | E(CDIH)=2.565 E(NOE )=59.298 E(PLAN)=15.103 | ------------------------------------------------------------------------------- %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 61866 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61847 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 61897 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 61911 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 1.41 A apart NBONDS: found 61962 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 62010 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 1.45 A apart NBONDS: found 62049 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 62096 intra-atom interactions NBONDS: found 62102 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62069 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=928.427 E(kin)=641.360 temperature=317.821 | | Etotal =287.067 grad(E)=66.376 E(BOND)=192.038 E(ANGL)=337.820 | | E(DIHE)=0.000 E(IMPR)=93.034 E(VDW )=-267.597 E(ELEC)=-151.515 | | E(CDIH)=3.036 E(NOE )=64.633 E(PLAN)=15.618 | ------------------------------------------------------------------------------- NBONDS: found 62077 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62013 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 62019 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 61949 intra-atom interactions NBONDS: found 61925 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=923.490 E(kin)=610.740 temperature=302.647 | | Etotal =312.751 grad(E)=68.411 E(BOND)=214.614 E(ANGL)=341.359 | | E(DIHE)=0.000 E(IMPR)=88.806 E(VDW )=-270.672 E(ELEC)=-139.050 | | E(CDIH)=0.364 E(NOE )=60.183 E(PLAN)=17.147 | ------------------------------------------------------------------------------- NBONDS: found 61894 intra-atom interactions NBONDS: found 61943 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 61934 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 61935 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 61966 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61932 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61899 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=936.643 E(kin)=584.341 temperature=289.566 | | Etotal =352.302 grad(E)=71.273 E(BOND)=231.215 E(ANGL)=355.122 | | E(DIHE)=0.000 E(IMPR)=98.350 E(VDW )=-261.142 E(ELEC)=-149.168 | | E(CDIH)=2.151 E(NOE )=60.895 E(PLAN)=14.880 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61919 intra-atom interactions NBONDS: found 61856 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61837 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 61883 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61909 intra-atom interactions NBONDS: found 61912 intra-atom interactions %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.48 A apart NBONDS: found 61940 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=923.690 E(kin)=601.812 temperature=298.223 | | Etotal =321.878 grad(E)=69.267 E(BOND)=207.451 E(ANGL)=357.144 | | E(DIHE)=0.000 E(IMPR)=90.217 E(VDW )=-257.937 E(ELEC)=-154.265 | | E(CDIH)=2.572 E(NOE )=58.356 E(PLAN)=18.341 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.988 E(kin)=605.515 temperature=300.058 | | Etotal =325.473 grad(E)=69.213 E(BOND)=221.624 E(ANGL)=345.139 | | E(DIHE)=0.000 E(IMPR)=91.523 E(VDW )=-263.379 E(ELEC)=-145.592 | | E(CDIH)=1.963 E(NOE )=58.405 E(PLAN)=15.791 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.263 E(kin)=12.539 temperature=6.214 | | Etotal =14.650 grad(E)=1.539 E(BOND)=9.880 E(ANGL)=10.993 | | E(DIHE)=0.000 E(IMPR)=6.528 E(VDW )=5.109 E(ELEC)=3.900 | | E(CDIH)=1.306 E(NOE )=5.870 E(PLAN)=1.753 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=930.480 E(kin)=605.336 temperature=299.969 | | Etotal =325.144 grad(E)=68.197 E(BOND)=216.968 E(ANGL)=341.606 | | E(DIHE)=0.000 E(IMPR)=90.912 E(VDW )=-262.337 E(ELEC)=-141.321 | | E(CDIH)=1.935 E(NOE )=61.506 E(PLAN)=15.875 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=14.236 E(kin)=13.506 temperature=6.693 | | Etotal =16.600 grad(E)=1.826 E(BOND)=10.908 E(ANGL)=12.679 | | E(DIHE)=0.000 E(IMPR)=6.678 E(VDW )=5.575 E(ELEC)=5.830 | | E(CDIH)=1.348 E(NOE )=6.904 E(PLAN)=2.030 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O5' " and "A -11 -ADE -H8 " only 1.47 A apart NBONDS: found 61945 intra-atom interactions NBONDS: found 61921 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61942 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 61914 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61916 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61925 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=923.908 E(kin)=586.979 temperature=290.873 | | Etotal =336.929 grad(E)=70.113 E(BOND)=213.100 E(ANGL)=366.228 | | E(DIHE)=0.000 E(IMPR)=87.920 E(VDW )=-257.851 E(ELEC)=-146.062 | | E(CDIH)=1.491 E(NOE )=57.614 E(PLAN)=14.488 | ------------------------------------------------------------------------------- %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 61873 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61820 intra-atom interactions NBONDS: found 61808 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61785 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 61814 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=923.098 E(kin)=593.295 temperature=294.003 | | Etotal =329.803 grad(E)=68.066 E(BOND)=200.070 E(ANGL)=368.038 | | E(DIHE)=0.000 E(IMPR)=87.330 E(VDW )=-260.974 E(ELEC)=-144.312 | | E(CDIH)=0.732 E(NOE )=64.762 E(PLAN)=14.158 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61850 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 61887 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 61866 intra-atom interactions NBONDS: found 61865 intra-atom interactions NBONDS: found 61894 intra-atom interactions NBONDS: found 61931 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=929.276 E(kin)=590.328 temperature=292.532 | | Etotal =338.948 grad(E)=69.150 E(BOND)=221.042 E(ANGL)=336.462 | | E(DIHE)=0.000 E(IMPR)=94.867 E(VDW )=-271.976 E(ELEC)=-141.855 | | E(CDIH)=1.035 E(NOE )=78.241 E(PLAN)=21.133 | ------------------------------------------------------------------------------- %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.50 A apart NBONDS: found 62009 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 1.45 A apart NBONDS: found 62011 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 1.40 A apart NBONDS: found 61960 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 61896 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 1.49 A apart NBONDS: found 61847 intra-atom interactions NBONDS: found 61859 intra-atom interactions NBONDS: found 61817 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=931.917 E(kin)=602.007 temperature=298.320 | | Etotal =329.911 grad(E)=68.890 E(BOND)=214.531 E(ANGL)=354.617 | | E(DIHE)=0.000 E(IMPR)=96.793 E(VDW )=-266.292 E(ELEC)=-144.036 | | E(CDIH)=3.390 E(NOE )=55.829 E(PLAN)=15.078 | ------------------------------------------------------------------------------- NBONDS: found 61865 intra-atom interactions NBONDS: found 61901 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61925 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 61957 intra-atom interactions %atoms "A -9 -URI -O2 " and "A -11 -ADE -H1' " only 1.50 A apart NBONDS: found 61999 intra-atom interactions NBONDS: found 61996 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=927.033 E(kin)=596.726 temperature=295.703 | | Etotal =330.307 grad(E)=68.439 E(BOND)=214.515 E(ANGL)=349.250 | | E(DIHE)=0.000 E(IMPR)=96.457 E(VDW )=-264.417 E(ELEC)=-144.427 | | E(CDIH)=1.205 E(NOE )=59.385 E(PLAN)=18.339 | ------------------------------------------------------------------------------- %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 1.47 A apart NBONDS: found 62038 intra-atom interactions NBONDS: found 62118 intra-atom interactions NBONDS: found 62117 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62119 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 62131 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 62158 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 62154 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=932.632 E(kin)=616.498 temperature=305.500 | | Etotal =316.135 grad(E)=68.153 E(BOND)=226.490 E(ANGL)=331.302 | | E(DIHE)=0.000 E(IMPR)=91.661 E(VDW )=-264.223 E(ELEC)=-144.918 | | E(CDIH)=1.025 E(NOE )=58.225 E(PLAN)=16.571 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 62209 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 62200 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62231 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62238 intra-atom interactions NBONDS: found 62156 intra-atom interactions NBONDS: found 62169 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 62150 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=924.000 E(kin)=605.133 temperature=299.869 | | Etotal =318.867 grad(E)=70.490 E(BOND)=226.612 E(ANGL)=322.921 | | E(DIHE)=0.000 E(IMPR)=98.797 E(VDW )=-261.084 E(ELEC)=-138.913 | | E(CDIH)=1.329 E(NOE )=54.284 E(PLAN)=14.920 | ------------------------------------------------------------------------------- %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 62200 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 62195 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62189 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62240 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62182 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=922.255 E(kin)=594.732 temperature=294.715 | | Etotal =327.523 grad(E)=69.793 E(BOND)=214.662 E(ANGL)=366.675 | | E(DIHE)=0.000 E(IMPR)=93.459 E(VDW )=-269.013 E(ELEC)=-152.751 | | E(CDIH)=0.608 E(NOE )=58.963 E(PLAN)=14.920 | ------------------------------------------------------------------------------- %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 62151 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62146 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 62088 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 62097 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 62104 intra-atom interactions NBONDS: found 62146 intra-atom interactions NBONDS: found 62154 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=949.040 E(kin)=603.135 temperature=298.879 | | Etotal =345.905 grad(E)=69.523 E(BOND)=212.234 E(ANGL)=359.006 | | E(DIHE)=0.000 E(IMPR)=103.309 E(VDW )=-269.459 E(ELEC)=-145.980 | | E(CDIH)=0.465 E(NOE )=69.110 E(PLAN)=17.220 | ------------------------------------------------------------------------------- NBONDS: found 62182 intra-atom interactions NBONDS: found 62177 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 62209 intra-atom interactions %atoms "A -12 -URI -O5' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62209 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 62149 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 62133 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 62155 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=925.882 E(kin)=606.941 temperature=300.765 | | Etotal =318.940 grad(E)=69.311 E(BOND)=217.605 E(ANGL)=327.677 | | E(DIHE)=0.000 E(IMPR)=103.345 E(VDW )=-270.013 E(ELEC)=-143.217 | | E(CDIH)=0.653 E(NOE )=66.360 E(PLAN)=16.530 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=930.163 E(kin)=605.491 temperature=300.046 | | Etotal =324.672 grad(E)=68.591 E(BOND)=216.120 E(ANGL)=348.459 | | E(DIHE)=0.000 E(IMPR)=91.497 E(VDW )=-263.950 E(ELEC)=-144.775 | | E(CDIH)=1.895 E(NOE )=59.613 E(PLAN)=15.814 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.313 E(kin)=13.113 temperature=6.498 | | Etotal =14.601 grad(E)=1.545 E(BOND)=10.010 E(ANGL)=12.212 | | E(DIHE)=0.000 E(IMPR)=6.559 E(VDW )=4.815 E(ELEC)=4.611 | | E(CDIH)=1.262 E(NOE )=6.229 E(PLAN)=1.892 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=930.460 E(kin)=605.346 temperature=299.974 | | Etotal =325.114 grad(E)=68.221 E(BOND)=216.915 E(ANGL)=342.035 | | E(DIHE)=0.000 E(IMPR)=90.948 E(VDW )=-262.438 E(ELEC)=-141.537 | | E(CDIH)=1.933 E(NOE )=61.388 E(PLAN)=15.871 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=13.905 E(kin)=13.482 temperature=6.681 | | Etotal =16.482 grad(E)=1.812 E(BOND)=10.856 E(ANGL)=12.759 | | E(DIHE)=0.000 E(IMPR)=6.672 E(VDW )=5.544 E(ELEC)=5.822 | | E(CDIH)=1.343 E(NOE )=6.879 E(PLAN)=2.022 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.07379 0.04041 0.01162 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR>close refine.tra end %X-PLOR>-ERR: File refine.tra was not open. X-PLOR> X-PLOR>! Compute dynamics average over second half of trajectory. X-PLOR> X-PLOR>evaluate ($steps2=$steps/2) EVALUATE: symbol $STEPS2 set to 20000.0 (real) X-PLOR>dynamics analysis average AVECOR> input=refine.tra ASSFIL: file /csb/pbm/0/dcs/ws/xplor/italy2/refine.tra opened. AVECOR> begin=$steps2 AVECOR> skip=200 AVECOR> stop=$steps AVECOR>end REMARKS FILENAME="/csb/pbm/0/dcs/ws/xplor/italy2/refine.tra" REMARKS DATE:17-Aug-96 07:12:57 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 NBONDS: found 62035 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 62028 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =-258.158 grad(E)=7.441 E(BOND)=13.753 E(ANGL)=92.391 | | E(DIHE)=0.000 E(IMPR)=13.676 E(VDW )=-271.499 E(ELEC)=-148.439 | | E(CDIH)=0.251 E(NOE )=27.985 E(PLAN)=13.724 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =-279.636 grad(E)=2.467 E(BOND)=7.304 E(ANGL)=78.477 | | E(DIHE)=0.000 E(IMPR)=13.055 E(VDW )=-271.978 E(ELEC)=-148.441 | | E(CDIH)=0.255 E(NOE )=28.561 E(PLAN)=13.131 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =-285.541 grad(E)=2.075 E(BOND)=6.820 E(ANGL)=76.242 | | E(DIHE)=0.000 E(IMPR)=12.659 E(VDW )=-272.476 E(ELEC)=-150.660 | | E(CDIH)=0.247 E(NOE )=29.294 E(PLAN)=12.333 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =-287.665 grad(E)=1.510 E(BOND)=6.917 E(ANGL)=75.497 | | E(DIHE)=0.000 E(IMPR)=12.605 E(VDW )=-272.751 E(ELEC)=-151.832 | | E(CDIH)=0.218 E(NOE )=29.651 E(PLAN)=12.030 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =-289.239 grad(E)=0.733 E(BOND)=6.814 E(ANGL)=75.388 | | E(DIHE)=0.000 E(IMPR)=12.702 E(VDW )=-272.807 E(ELEC)=-153.400 | | E(CDIH)=0.274 E(NOE )=30.116 E(PLAN)=11.673 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =-290.320 grad(E)=1.066 E(BOND)=6.865 E(ANGL)=76.401 | | E(DIHE)=0.000 E(IMPR)=12.565 E(VDW )=-273.062 E(ELEC)=-155.386 | | E(CDIH)=0.342 E(NOE )=30.528 E(PLAN)=11.429 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =-291.452 grad(E)=0.970 E(BOND)=6.830 E(ANGL)=76.991 | | E(DIHE)=0.000 E(IMPR)=12.768 E(VDW )=-273.160 E(ELEC)=-157.068 | | E(CDIH)=0.335 E(NOE )=30.422 E(PLAN)=11.429 | ------------------------------------------------------------------------------- NBONDS: found 62056 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =-292.234 grad(E)=0.764 E(BOND)=6.868 E(ANGL)=76.562 | | E(DIHE)=0.000 E(IMPR)=12.984 E(VDW )=-273.004 E(ELEC)=-158.195 | | E(CDIH)=0.301 E(NOE )=30.715 E(PLAN)=11.535 | ------------------------------------------------------------------------------- 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 $RMS_BOND set to 0.213513E-02 (real) X-PLOR>evaluate ($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 $RMS_ANGL set to 0.637426 (real) X-PLOR>evaluate ($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 $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.363 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.363439 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 12 URI H1' set-j-atoms A 13 ADE H8 R= 5.285 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.285 E(NOE)= 8.139 NOEPRI: RMS diff. = 0.018, #(violat.> 0.2)= 1 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.018, #(viol.> 0.2)= 1 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.181928E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 1.00000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 0 RMS deviation= 0.078 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.780080E-01 (real) X-PLOR>evaluate ($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 6.86849, angle 76.5621, dihedral 0, improper 12.9839, NOE 30.7148, c-dihedral 0.301037, planar 11.5348, VdW -273.004, elec -158.195, total -292.234 RMSD: bond 2.135129E-03, angle 0.637426, dihedral 0, improper 0.363439, NOE 1.819282E-02, c-dihedral 7.800802E-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= 134448 current use= 0 X-PLOR: total CPU time= 2829.6641 s X-PLOR: entry time at 07:12:25 17-Aug-96 X-PLOR: exit time at 07:59:53 17-Aug-96