X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 08:02:39 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=114082.478668213 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 19:43:15 created by user: COOR>ATOM 1 P GUA A 1 -6.552 9.677 3.601 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -5.404 8.806 3.960 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 -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61695 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =84.181 grad(E)=4.715 E(BOND)=18.977 E(ANGL)=155.998 | | E(DIHE)=0.000 E(IMPR)=15.916 E(VDW )=-170.670 E(ELEC)=-91.091 | | E(CDIH)=5.435 E(NOE )=140.476 E(PLAN)=9.141 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =70.448 grad(E)=2.324 E(BOND)=20.298 E(ANGL)=158.937 | | E(DIHE)=0.000 E(IMPR)=17.080 E(VDW )=-187.184 E(ELEC)=-94.737 | | E(CDIH)=5.260 E(NOE )=140.321 E(PLAN)=10.473 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =60.233 grad(E)=3.257 E(BOND)=18.452 E(ANGL)=158.101 | | E(DIHE)=0.000 E(IMPR)=18.352 E(VDW )=-187.611 E(ELEC)=-98.651 | | E(CDIH)=4.672 E(NOE )=135.606 E(PLAN)=11.313 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =51.038 grad(E)=2.136 E(BOND)=17.824 E(ANGL)=158.284 | | E(DIHE)=0.000 E(IMPR)=19.732 E(VDW )=-188.370 E(ELEC)=-104.975 | | E(CDIH)=5.243 E(NOE )=131.462 E(PLAN)=11.837 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =43.385 grad(E)=2.812 E(BOND)=17.395 E(ANGL)=159.264 | | E(DIHE)=0.000 E(IMPR)=19.765 E(VDW )=-191.084 E(ELEC)=-112.123 | | E(CDIH)=5.527 E(NOE )=132.753 E(PLAN)=11.889 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61873 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =36.432 grad(E)=2.445 E(BOND)=17.898 E(ANGL)=158.805 | | E(DIHE)=0.000 E(IMPR)=17.552 E(VDW )=-190.948 E(ELEC)=-118.390 | | E(CDIH)=4.681 E(NOE )=134.701 E(PLAN)=12.134 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =29.884 grad(E)=2.465 E(BOND)=17.255 E(ANGL)=159.456 | | E(DIHE)=0.000 E(IMPR)=16.779 E(VDW )=-191.129 E(ELEC)=-122.362 | | E(CDIH)=4.263 E(NOE )=133.973 E(PLAN)=11.649 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =23.125 grad(E)=2.123 E(BOND)=17.006 E(ANGL)=157.087 | | E(DIHE)=0.000 E(IMPR)=16.172 E(VDW )=-192.237 E(ELEC)=-125.725 | | E(CDIH)=3.594 E(NOE )=136.091 E(PLAN)=11.138 | ------------------------------------------------------------------------------- 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= 0.204824598E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.08737 0.00469 0.04518 velocity [A/ps] : -0.10612 0.41754 -0.09173 ang. mom. [amu A/ps] : -2756.79481 9754.96712 -37126.15331 kin. ener. [Kcal/mol] : 1.56384 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.08737 0.00469 0.04518 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)=651.910 E(kin)=628.785 temperature=311.589 | | Etotal =23.125 grad(E)=2.123 E(BOND)=17.006 E(ANGL)=157.087 | | E(DIHE)=0.000 E(IMPR)=16.172 E(VDW )=-192.237 E(ELEC)=-125.725 | | E(CDIH)=3.594 E(NOE )=136.091 E(PLAN)=11.138 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61913 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61911 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61879 intra-atom interactions %atoms "A -10 -CYT -O3' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61828 intra-atom interactions %atoms "A -10 -CYT -O3' " and "A -11 -ADE -H8 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61786 intra-atom interactions %atoms "A -10 -CYT -O3' " and "A -11 -ADE -H8 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61746 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61697 intra-atom interactions NBONDS: found 61605 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61561 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61537 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61488 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61423 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=1248.905 E(kin)=599.005 temperature=296.832 | | Etotal =649.900 grad(E)=66.810 E(BOND)=207.437 E(ANGL)=433.544 | | E(DIHE)=0.000 E(IMPR)=96.906 E(VDW )=-185.527 E(ELEC)=-104.443 | | E(CDIH)=7.409 E(NOE )=184.701 E(PLAN)=9.872 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61359 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61247 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61256 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61255 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61273 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61293 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61227 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61222 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61184 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61170 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61110 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=1181.910 E(kin)=591.151 temperature=292.940 | | Etotal =590.759 grad(E)=67.429 E(BOND)=213.959 E(ANGL)=422.284 | | E(DIHE)=0.000 E(IMPR)=102.475 E(VDW )=-202.819 E(ELEC)=-127.235 | | E(CDIH)=2.540 E(NOE )=163.008 E(PLAN)=16.547 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61030 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 60913 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 60779 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60751 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60636 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -14 -ADE -HO2'" and "A -15 -CYT -H5' " only 1.49 A apart NBONDS: found 60578 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 60509 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 60483 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=1183.784 E(kin)=599.365 temperature=297.010 | | Etotal =584.419 grad(E)=64.703 E(BOND)=199.705 E(ANGL)=426.149 | | E(DIHE)=0.000 E(IMPR)=97.375 E(VDW )=-204.955 E(ELEC)=-136.903 | | E(CDIH)=5.454 E(NOE )=177.066 E(PLAN)=20.530 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 60501 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 60462 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.18 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 60427 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 60266 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60200 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 60143 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 60075 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60062 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 60052 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 59996 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60017 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=1148.175 E(kin)=590.659 temperature=292.696 | | Etotal =557.517 grad(E)=66.355 E(BOND)=196.372 E(ANGL)=405.200 | | E(DIHE)=0.000 E(IMPR)=102.847 E(VDW )=-204.266 E(ELEC)=-118.643 | | E(CDIH)=4.762 E(NOE )=154.512 E(PLAN)=16.733 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 60018 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 60073 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 60113 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 60192 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 60271 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 60334 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 60407 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 60489 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60552 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 60513 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 60570 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=1188.619 E(kin)=622.947 temperature=308.696 | | Etotal =565.672 grad(E)=65.507 E(BOND)=186.691 E(ANGL)=392.837 | | E(DIHE)=0.000 E(IMPR)=97.292 E(VDW )=-198.633 E(ELEC)=-107.899 | | E(CDIH)=4.344 E(NOE )=179.897 E(PLAN)=11.143 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 60594 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 60555 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60535 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60534 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.43 A apart %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 60600 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.50 A apart NBONDS: found 60620 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart NBONDS: found 60678 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 60683 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 60680 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 60739 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 60725 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=1185.268 E(kin)=609.854 temperature=302.208 | | Etotal =575.415 grad(E)=68.092 E(BOND)=201.786 E(ANGL)=379.363 | | E(DIHE)=0.000 E(IMPR)=107.848 E(VDW )=-199.173 E(ELEC)=-118.495 | | E(CDIH)=8.892 E(NOE )=179.964 E(PLAN)=15.230 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60701 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 60733 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60727 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60751 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60695 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 60740 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 60694 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 60734 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.20 A apart NBONDS: found 60772 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.21 A apart NBONDS: found 60835 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 60884 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60950 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 60916 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 60941 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=1158.473 E(kin)=615.662 temperature=305.087 | | Etotal =542.811 grad(E)=64.909 E(BOND)=174.648 E(ANGL)=436.970 | | E(DIHE)=0.000 E(IMPR)=85.603 E(VDW )=-192.633 E(ELEC)=-128.821 | | E(CDIH)=3.016 E(NOE )=149.159 E(PLAN)=14.870 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60942 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 60938 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60956 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60976 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 60933 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 60958 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.21 A apart NBONDS: found 61017 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61040 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61074 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61093 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61100 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61124 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61134 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61120 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61134 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61123 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61107 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61085 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=1165.326 E(kin)=622.715 temperature=308.581 | | Etotal =542.612 grad(E)=64.098 E(BOND)=196.895 E(ANGL)=384.047 | | E(DIHE)=0.000 E(IMPR)=95.329 E(VDW )=-193.769 E(ELEC)=-121.366 | | E(CDIH)=3.010 E(NOE )=161.502 E(PLAN)=16.965 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61111 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61107 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61157 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61186 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61271 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61306 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61425 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61482 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61550 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61584 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=1163.898 E(kin)=614.308 temperature=304.415 | | Etotal =549.590 grad(E)=63.831 E(BOND)=208.287 E(ANGL)=396.818 | | E(DIHE)=0.000 E(IMPR)=88.045 E(VDW )=-180.243 E(ELEC)=-128.559 | | E(CDIH)=9.042 E(NOE )=138.809 E(PLAN)=17.392 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61683 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61693 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61741 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61814 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61838 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61879 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61924 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61859 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61809 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=1178.793 E(kin)=636.964 temperature=315.642 | | Etotal =541.829 grad(E)=64.235 E(BOND)=192.870 E(ANGL)=418.868 | | E(DIHE)=0.000 E(IMPR)=85.573 E(VDW )=-185.738 E(ELEC)=-125.226 | | E(CDIH)=2.958 E(NOE )=137.602 E(PLAN)=14.922 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1175.000 E(kin)=603.512 temperature=299.065 | | Etotal =571.488 grad(E)=65.342 E(BOND)=206.189 E(ANGL)=400.935 | | E(DIHE)=0.000 E(IMPR)=93.743 E(VDW )=-194.848 E(ELEC)=-121.674 | | E(CDIH)=4.619 E(NOE )=166.135 E(PLAN)=16.389 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=40.624 E(kin)=21.649 temperature=10.728 | | Etotal =32.090 grad(E)=1.891 E(BOND)=12.248 E(ANGL)=19.099 | | E(DIHE)=0.000 E(IMPR)=7.934 E(VDW )=10.454 E(ELEC)=8.971 | | E(CDIH)=2.257 E(NOE )=13.067 E(PLAN)=2.464 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61684 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61578 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61509 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61465 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61489 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61477 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61502 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=1162.668 E(kin)=596.235 temperature=295.459 | | Etotal =566.433 grad(E)=66.220 E(BOND)=212.350 E(ANGL)=417.789 | | E(DIHE)=0.000 E(IMPR)=96.289 E(VDW )=-199.632 E(ELEC)=-117.716 | | E(CDIH)=3.418 E(NOE )=140.104 E(PLAN)=13.830 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61567 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61642 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61634 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61708 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.47 A apart NBONDS: found 61664 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61649 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61707 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=1173.236 E(kin)=611.599 temperature=303.073 | | Etotal =561.637 grad(E)=63.871 E(BOND)=216.375 E(ANGL)=405.970 | | E(DIHE)=0.000 E(IMPR)=83.096 E(VDW )=-186.783 E(ELEC)=-128.187 | | E(CDIH)=5.669 E(NOE )=151.426 E(PLAN)=14.072 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61732 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61763 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 61824 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61880 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61914 intra-atom interactions NBONDS: found 61927 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61875 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61859 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=1178.111 E(kin)=626.562 temperature=310.488 | | Etotal =551.549 grad(E)=65.645 E(BOND)=193.261 E(ANGL)=373.555 | | E(DIHE)=0.000 E(IMPR)=96.122 E(VDW )=-184.457 E(ELEC)=-132.992 | | E(CDIH)=4.231 E(NOE )=180.891 E(PLAN)=20.938 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61879 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61851 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61908 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61935 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61977 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62030 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62147 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 62169 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=1187.689 E(kin)=583.883 temperature=289.339 | | Etotal =603.805 grad(E)=66.307 E(BOND)=230.034 E(ANGL)=403.840 | | E(DIHE)=0.000 E(IMPR)=102.923 E(VDW )=-174.858 E(ELEC)=-132.339 | | E(CDIH)=2.560 E(NOE )=156.057 E(PLAN)=15.589 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.20 A apart NBONDS: found 62218 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 62202 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62225 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62210 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62179 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62161 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62133 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.45 A apart NBONDS: found 62039 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61973 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61935 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61828 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=1151.873 E(kin)=589.909 temperature=292.325 | | Etotal =561.964 grad(E)=65.363 E(BOND)=202.366 E(ANGL)=407.909 | | E(DIHE)=0.000 E(IMPR)=96.049 E(VDW )=-194.529 E(ELEC)=-124.520 | | E(CDIH)=5.883 E(NOE )=155.766 E(PLAN)=13.041 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61696 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61653 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61717 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61764 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61786 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61833 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61893 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=1166.171 E(kin)=601.332 temperature=297.985 | | Etotal =564.839 grad(E)=62.716 E(BOND)=210.788 E(ANGL)=402.303 | | E(DIHE)=0.000 E(IMPR)=69.000 E(VDW )=-192.688 E(ELEC)=-135.577 | | E(CDIH)=4.145 E(NOE )=192.861 E(PLAN)=14.008 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61927 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61954 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61857 intra-atom interactions NBONDS: found 61766 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61610 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61544 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61515 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=1171.446 E(kin)=613.614 temperature=304.072 | | Etotal =557.832 grad(E)=63.943 E(BOND)=219.683 E(ANGL)=411.251 | | E(DIHE)=0.000 E(IMPR)=86.357 E(VDW )=-186.897 E(ELEC)=-126.672 | | E(CDIH)=3.456 E(NOE )=133.389 E(PLAN)=17.265 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61471 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61446 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61384 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61460 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61393 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61490 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61501 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=1174.614 E(kin)=620.914 temperature=307.689 | | Etotal =553.700 grad(E)=62.808 E(BOND)=200.751 E(ANGL)=406.692 | | E(DIHE)=0.000 E(IMPR)=101.511 E(VDW )=-193.131 E(ELEC)=-135.768 | | E(CDIH)=2.892 E(NOE )=151.988 E(PLAN)=18.765 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61473 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61486 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61532 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61615 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61640 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=1129.785 E(kin)=595.995 temperature=295.341 | | Etotal =533.790 grad(E)=63.117 E(BOND)=201.177 E(ANGL)=387.633 | | E(DIHE)=0.000 E(IMPR)=91.877 E(VDW )=-176.643 E(ELEC)=-133.882 | | E(CDIH)=5.693 E(NOE )=141.498 E(PLAN)=16.437 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61706 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61754 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61848 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61838 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61896 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61807 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61739 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=1178.562 E(kin)=595.017 temperature=294.856 | | Etotal =583.545 grad(E)=64.426 E(BOND)=223.846 E(ANGL)=402.909 | | E(DIHE)=0.000 E(IMPR)=87.190 E(VDW )=-189.336 E(ELEC)=-128.172 | | E(CDIH)=1.573 E(NOE )=169.623 E(PLAN)=15.912 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1172.852 E(kin)=605.461 temperature=300.032 | | Etotal =567.390 grad(E)=64.762 E(BOND)=213.463 E(ANGL)=398.899 | | E(DIHE)=0.000 E(IMPR)=92.572 E(VDW )=-186.797 E(ELEC)=-129.070 | | E(CDIH)=3.686 E(NOE )=158.067 E(PLAN)=16.570 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=15.758 E(kin)=12.065 temperature=5.979 | | Etotal =19.496 grad(E)=1.357 E(BOND)=9.429 E(ANGL)=17.293 | | E(DIHE)=0.000 E(IMPR)=6.788 E(VDW )=10.437 E(ELEC)=5.520 | | E(CDIH)=1.960 E(NOE )=13.779 E(PLAN)=2.294 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=1173.926 E(kin)=604.487 temperature=299.548 | | Etotal =569.439 grad(E)=65.052 E(BOND)=209.826 E(ANGL)=399.917 | | E(DIHE)=0.000 E(IMPR)=93.158 E(VDW )=-190.822 E(ELEC)=-125.372 | | E(CDIH)=4.152 E(NOE )=162.101 E(PLAN)=16.480 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=30.829 E(kin)=17.552 temperature=8.698 | | Etotal =26.630 grad(E)=1.671 E(BOND)=11.519 E(ANGL)=18.247 | | E(DIHE)=0.000 E(IMPR)=7.407 E(VDW )=11.194 E(ELEC)=8.316 | | E(CDIH)=2.164 E(NOE )=14.020 E(PLAN)=2.382 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61758 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61736 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61732 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61765 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61718 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61682 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61642 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=1165.189 E(kin)=581.806 temperature=288.309 | | Etotal =583.384 grad(E)=67.097 E(BOND)=227.939 E(ANGL)=392.558 | | E(DIHE)=0.000 E(IMPR)=103.030 E(VDW )=-191.988 E(ELEC)=-123.380 | | E(CDIH)=7.173 E(NOE )=153.269 E(PLAN)=14.782 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61526 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61451 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61406 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61372 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61321 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61249 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61189 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61175 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=1172.512 E(kin)=595.553 temperature=295.122 | | Etotal =576.959 grad(E)=65.058 E(BOND)=205.434 E(ANGL)=419.671 | | E(DIHE)=0.000 E(IMPR)=97.328 E(VDW )=-197.270 E(ELEC)=-126.871 | | E(CDIH)=3.555 E(NOE )=158.471 E(PLAN)=16.642 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61103 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61065 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61065 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61006 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61011 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 60969 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61003 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61032 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61134 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=1157.861 E(kin)=594.263 temperature=294.482 | | Etotal =563.599 grad(E)=64.105 E(BOND)=220.498 E(ANGL)=398.246 | | E(DIHE)=0.000 E(IMPR)=91.822 E(VDW )=-185.131 E(ELEC)=-131.466 | | E(CDIH)=3.799 E(NOE )=149.176 E(PLAN)=16.655 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61137 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61096 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61008 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 60905 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 60843 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60813 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 60811 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 60881 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=1172.173 E(kin)=608.457 temperature=301.516 | | Etotal =563.716 grad(E)=65.447 E(BOND)=224.701 E(ANGL)=383.244 | | E(DIHE)=0.000 E(IMPR)=86.710 E(VDW )=-180.429 E(ELEC)=-127.120 | | E(CDIH)=3.102 E(NOE )=155.833 E(PLAN)=17.675 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -12 -URI -O2' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 60894 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 60966 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61011 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61061 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61125 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61184 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61207 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61230 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=1178.039 E(kin)=615.171 temperature=304.843 | | Etotal =562.868 grad(E)=64.136 E(BOND)=228.676 E(ANGL)=393.054 | | E(DIHE)=0.000 E(IMPR)=90.418 E(VDW )=-192.622 E(ELEC)=-126.405 | | E(CDIH)=0.787 E(NOE )=153.145 E(PLAN)=15.813 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61277 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61285 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61261 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61285 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61275 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61270 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61199 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=1186.801 E(kin)=627.260 temperature=310.834 | | Etotal =559.540 grad(E)=62.434 E(BOND)=230.329 E(ANGL)=394.532 | | E(DIHE)=0.000 E(IMPR)=85.892 E(VDW )=-201.828 E(ELEC)=-121.600 | | E(CDIH)=4.120 E(NOE )=151.336 E(PLAN)=16.759 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61154 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61124 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61127 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61258 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61281 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61387 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=1174.329 E(kin)=605.875 temperature=300.237 | | Etotal =568.454 grad(E)=63.864 E(BOND)=221.477 E(ANGL)=398.887 | | E(DIHE)=0.000 E(IMPR)=92.276 E(VDW )=-192.723 E(ELEC)=-127.611 | | E(CDIH)=3.151 E(NOE )=155.526 E(PLAN)=17.471 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61437 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61601 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61715 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.32 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61770 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.38 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61824 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61830 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61805 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61799 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=1172.514 E(kin)=611.466 temperature=303.007 | | Etotal =561.049 grad(E)=64.700 E(BOND)=215.223 E(ANGL)=405.706 | | E(DIHE)=0.000 E(IMPR)=89.047 E(VDW )=-182.709 E(ELEC)=-127.210 | | E(CDIH)=6.127 E(NOE )=139.965 E(PLAN)=14.900 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61687 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61620 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61582 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61557 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61536 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61474 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61440 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61398 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=1152.528 E(kin)=606.074 temperature=300.335 | | Etotal =546.454 grad(E)=66.420 E(BOND)=217.294 E(ANGL)=372.338 | | E(DIHE)=0.000 E(IMPR)=88.251 E(VDW )=-183.569 E(ELEC)=-128.273 | | E(CDIH)=3.475 E(NOE )=161.263 E(PLAN)=15.674 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61454 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.20 A apart NBONDS: found 61448 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61368 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61336 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61320 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61306 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61343 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61331 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61389 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=1165.172 E(kin)=600.847 temperature=297.745 | | Etotal =564.325 grad(E)=66.488 E(BOND)=235.117 E(ANGL)=395.194 | | E(DIHE)=0.000 E(IMPR)=84.929 E(VDW )=-201.437 E(ELEC)=-129.951 | | E(CDIH)=4.560 E(NOE )=160.063 E(PLAN)=15.850 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1170.013 E(kin)=605.531 temperature=300.066 | | Etotal =564.482 grad(E)=65.018 E(BOND)=219.730 E(ANGL)=395.530 | | E(DIHE)=0.000 E(IMPR)=90.007 E(VDW )=-194.833 E(ELEC)=-124.852 | | E(CDIH)=3.551 E(NOE )=159.727 E(PLAN)=15.622 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.641 E(kin)=12.136 temperature=6.014 | | Etotal =16.395 grad(E)=1.331 E(BOND)=11.324 E(ANGL)=14.412 | | E(DIHE)=0.000 E(IMPR)=6.869 E(VDW )=9.002 E(ELEC)=3.624 | | E(CDIH)=1.864 E(NOE )=10.345 E(PLAN)=1.499 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=1172.622 E(kin)=604.835 temperature=299.721 | | Etotal =567.787 grad(E)=65.041 E(BOND)=213.127 E(ANGL)=398.455 | | E(DIHE)=0.000 E(IMPR)=92.107 E(VDW )=-192.159 E(ELEC)=-125.199 | | E(CDIH)=3.952 E(NOE )=161.310 E(PLAN)=16.194 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=26.119 E(kin)=15.960 temperature=7.909 | | Etotal =23.829 grad(E)=1.566 E(BOND)=12.369 E(ANGL)=17.189 | | E(DIHE)=0.000 E(IMPR)=7.383 E(VDW )=10.683 E(ELEC)=7.109 | | E(CDIH)=2.089 E(NOE )=12.960 E(PLAN)=2.167 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61343 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61334 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61337 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61339 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61212 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61237 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61194 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61117 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61086 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=1167.629 E(kin)=614.340 temperature=304.431 | | Etotal =553.289 grad(E)=63.972 E(BOND)=209.678 E(ANGL)=402.536 | | E(DIHE)=0.000 E(IMPR)=91.509 E(VDW )=-208.151 E(ELEC)=-131.784 | | E(CDIH)=1.990 E(NOE )=170.002 E(PLAN)=17.509 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61072 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61093 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61102 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61146 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61180 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61283 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61365 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=1153.408 E(kin)=600.947 temperature=297.795 | | Etotal =552.460 grad(E)=66.580 E(BOND)=242.054 E(ANGL)=380.282 | | E(DIHE)=0.000 E(IMPR)=87.899 E(VDW )=-212.502 E(ELEC)=-135.422 | | E(CDIH)=1.115 E(NOE )=172.291 E(PLAN)=16.743 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61442 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61526 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61567 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61649 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61680 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61653 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61680 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61672 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61631 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 61661 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=1168.689 E(kin)=609.371 temperature=301.969 | | Etotal =559.318 grad(E)=65.730 E(BOND)=226.923 E(ANGL)=392.436 | | E(DIHE)=0.000 E(IMPR)=97.123 E(VDW )=-200.984 E(ELEC)=-136.492 | | E(CDIH)=3.488 E(NOE )=160.752 E(PLAN)=16.072 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61635 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61538 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61401 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61264 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61223 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61150 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61124 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61151 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=1171.158 E(kin)=610.352 temperature=302.455 | | Etotal =560.806 grad(E)=65.392 E(BOND)=218.921 E(ANGL)=397.897 | | E(DIHE)=0.000 E(IMPR)=99.260 E(VDW )=-198.005 E(ELEC)=-131.286 | | E(CDIH)=6.519 E(NOE )=149.170 E(PLAN)=18.330 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61249 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61332 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61368 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61424 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61461 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61507 intra-atom interactions %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61598 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=1165.999 E(kin)=589.343 temperature=292.044 | | Etotal =576.656 grad(E)=67.158 E(BOND)=239.150 E(ANGL)=386.422 | | E(DIHE)=0.000 E(IMPR)=101.395 E(VDW )=-193.075 E(ELEC)=-135.517 | | E(CDIH)=7.175 E(NOE )=153.187 E(PLAN)=17.919 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 61650 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61638 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61635 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61599 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61553 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61597 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61720 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61761 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=1200.588 E(kin)=602.990 temperature=298.807 | | Etotal =597.599 grad(E)=65.944 E(BOND)=226.746 E(ANGL)=405.892 | | E(DIHE)=0.000 E(IMPR)=101.885 E(VDW )=-184.336 E(ELEC)=-135.319 | | E(CDIH)=5.220 E(NOE )=160.144 E(PLAN)=17.366 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61834 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61851 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61859 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61910 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61913 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61922 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61963 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61981 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=1182.037 E(kin)=595.877 temperature=295.282 | | Etotal =586.160 grad(E)=65.760 E(BOND)=230.780 E(ANGL)=398.130 | | E(DIHE)=0.000 E(IMPR)=110.242 E(VDW )=-188.852 E(ELEC)=-130.468 | | E(CDIH)=1.120 E(NOE )=152.542 E(PLAN)=12.666 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61998 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62033 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61993 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61926 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61836 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61778 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61767 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61750 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61731 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=1180.546 E(kin)=612.654 temperature=303.596 | | Etotal =567.892 grad(E)=67.949 E(BOND)=230.202 E(ANGL)=384.561 | | E(DIHE)=0.000 E(IMPR)=100.789 E(VDW )=-204.193 E(ELEC)=-128.820 | | E(CDIH)=3.651 E(NOE )=167.752 E(PLAN)=13.949 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61762 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61761 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61833 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61834 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61853 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61833 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61847 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61822 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61856 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61854 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61768 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=1166.513 E(kin)=603.630 temperature=299.124 | | Etotal =562.884 grad(E)=65.735 E(BOND)=219.179 E(ANGL)=399.465 | | E(DIHE)=0.000 E(IMPR)=95.239 E(VDW )=-190.080 E(ELEC)=-132.127 | | E(CDIH)=12.718 E(NOE )=142.188 E(PLAN)=16.301 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61703 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61640 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61662 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61612 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61586 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61471 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61361 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=1176.796 E(kin)=618.662 temperature=306.573 | | Etotal =558.134 grad(E)=65.294 E(BOND)=225.572 E(ANGL)=381.078 | | E(DIHE)=0.000 E(IMPR)=100.087 E(VDW )=-204.001 E(ELEC)=-137.640 | | E(CDIH)=2.507 E(NOE )=170.580 E(PLAN)=19.951 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1170.053 E(kin)=605.434 temperature=300.018 | | Etotal =564.620 grad(E)=65.917 E(BOND)=220.593 E(ANGL)=397.011 | | E(DIHE)=0.000 E(IMPR)=97.060 E(VDW )=-198.804 E(ELEC)=-132.214 | | E(CDIH)=3.712 E(NOE )=159.900 E(PLAN)=17.361 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=11.325 E(kin)=11.943 temperature=5.918 | | Etotal =16.074 grad(E)=1.381 E(BOND)=9.864 E(ANGL)=12.578 | | E(DIHE)=0.000 E(IMPR)=7.609 E(VDW )=7.998 E(ELEC)=4.023 | | E(CDIH)=2.013 E(NOE )=10.698 E(PLAN)=2.654 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=1171.979 E(kin)=604.985 temperature=299.795 | | Etotal =566.995 grad(E)=65.260 E(BOND)=214.994 E(ANGL)=398.094 | | E(DIHE)=0.000 E(IMPR)=93.345 E(VDW )=-193.821 E(ELEC)=-126.952 | | E(CDIH)=3.892 E(NOE )=160.957 E(PLAN)=16.486 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=23.344 E(kin)=15.059 temperature=7.462 | | Etotal =22.189 grad(E)=1.569 E(BOND)=12.228 E(ANGL)=16.172 | | E(DIHE)=0.000 E(IMPR)=7.743 E(VDW )=10.482 E(ELEC)=7.154 | | E(CDIH)=2.073 E(NOE )=12.448 E(PLAN)=2.353 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61303 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61299 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61294 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61300 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61337 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61457 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61531 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61618 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61596 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=1161.156 E(kin)=599.715 temperature=297.184 | | Etotal =561.441 grad(E)=63.631 E(BOND)=204.317 E(ANGL)=397.328 | | E(DIHE)=0.000 E(IMPR)=99.172 E(VDW )=-184.222 E(ELEC)=-132.052 | | E(CDIH)=4.918 E(NOE )=150.628 E(PLAN)=21.352 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61578 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61551 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61534 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61550 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61521 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61513 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61509 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61542 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=1145.428 E(kin)=609.606 temperature=302.086 | | Etotal =535.822 grad(E)=64.199 E(BOND)=226.024 E(ANGL)=389.327 | | E(DIHE)=0.000 E(IMPR)=86.409 E(VDW )=-201.987 E(ELEC)=-140.230 | | E(CDIH)=0.947 E(NOE )=159.098 E(PLAN)=16.234 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61543 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61592 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61569 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61655 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61604 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61622 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61628 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=1175.059 E(kin)=622.127 temperature=308.290 | | Etotal =552.933 grad(E)=63.851 E(BOND)=204.617 E(ANGL)=400.744 | | E(DIHE)=0.000 E(IMPR)=102.107 E(VDW )=-204.709 E(ELEC)=-129.888 | | E(CDIH)=3.128 E(NOE )=163.253 E(PLAN)=13.681 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61593 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61646 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61678 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61621 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61548 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61532 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61472 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61439 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=1138.814 E(kin)=590.821 temperature=292.776 | | Etotal =547.994 grad(E)=65.184 E(BOND)=221.562 E(ANGL)=385.556 | | E(DIHE)=0.000 E(IMPR)=93.930 E(VDW )=-206.791 E(ELEC)=-130.407 | | E(CDIH)=0.976 E(NOE )=169.745 E(PLAN)=13.423 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61439 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61413 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61440 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61474 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61507 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61527 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61583 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61697 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=1163.288 E(kin)=620.092 temperature=307.281 | | Etotal =543.197 grad(E)=65.200 E(BOND)=216.497 E(ANGL)=391.597 | | E(DIHE)=0.000 E(IMPR)=90.517 E(VDW )=-193.897 E(ELEC)=-131.272 | | E(CDIH)=1.752 E(NOE )=154.798 E(PLAN)=13.204 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61772 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61722 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61712 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61752 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61753 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61777 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=1174.180 E(kin)=621.033 temperature=307.748 | | Etotal =553.146 grad(E)=63.559 E(BOND)=212.932 E(ANGL)=412.024 | | E(DIHE)=0.000 E(IMPR)=91.977 E(VDW )=-194.902 E(ELEC)=-132.375 | | E(CDIH)=5.207 E(NOE )=142.621 E(PLAN)=15.663 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61843 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61873 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61899 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61931 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.20 A apart NBONDS: found 61983 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=1171.419 E(kin)=595.834 temperature=295.261 | | Etotal =575.585 grad(E)=67.488 E(BOND)=220.772 E(ANGL)=397.624 | | E(DIHE)=0.000 E(IMPR)=104.294 E(VDW )=-188.935 E(ELEC)=-132.308 | | E(CDIH)=3.673 E(NOE )=156.093 E(PLAN)=14.373 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 62012 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61996 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62045 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62003 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61866 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61874 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61774 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61743 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=1163.983 E(kin)=591.688 temperature=293.206 | | Etotal =572.295 grad(E)=67.146 E(BOND)=224.917 E(ANGL)=392.929 | | E(DIHE)=0.000 E(IMPR)=97.655 E(VDW )=-186.083 E(ELEC)=-125.542 | | E(CDIH)=1.757 E(NOE )=154.128 E(PLAN)=12.534 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61731 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61780 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61820 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61864 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61868 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61888 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61782 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=1178.282 E(kin)=605.860 temperature=300.229 | | Etotal =572.422 grad(E)=66.406 E(BOND)=218.835 E(ANGL)=406.559 | | E(DIHE)=0.000 E(IMPR)=107.346 E(VDW )=-193.973 E(ELEC)=-129.992 | | E(CDIH)=4.495 E(NOE )=145.547 E(PLAN)=13.605 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61722 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61630 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61528 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61513 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61437 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61397 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61364 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61355 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=1166.451 E(kin)=608.819 temperature=301.695 | | Etotal =557.633 grad(E)=66.875 E(BOND)=220.969 E(ANGL)=393.796 | | E(DIHE)=0.000 E(IMPR)=90.181 E(VDW )=-195.864 E(ELEC)=-124.429 | | E(CDIH)=1.675 E(NOE )=152.455 E(PLAN)=18.849 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1168.528 E(kin)=605.522 temperature=300.062 | | Etotal =563.006 grad(E)=66.330 E(BOND)=223.869 E(ANGL)=394.477 | | E(DIHE)=0.000 E(IMPR)=96.689 E(VDW )=-197.190 E(ELEC)=-130.740 | | E(CDIH)=3.482 E(NOE )=157.149 E(PLAN)=15.270 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.861 E(kin)=12.183 temperature=6.037 | | Etotal =15.939 grad(E)=1.460 E(BOND)=10.422 E(ANGL)=11.613 | | E(DIHE)=0.000 E(IMPR)=6.765 E(VDW )=7.668 E(ELEC)=4.354 | | E(CDIH)=1.720 E(NOE )=8.889 E(PLAN)=2.154 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=1171.289 E(kin)=605.092 temperature=299.849 | | Etotal =566.197 grad(E)=65.474 E(BOND)=216.769 E(ANGL)=397.370 | | E(DIHE)=0.000 E(IMPR)=94.014 E(VDW )=-194.494 E(ELEC)=-127.710 | | E(CDIH)=3.810 E(NOE )=160.196 E(PLAN)=16.242 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=21.482 E(kin)=14.531 temperature=7.201 | | Etotal =21.148 grad(E)=1.606 E(BOND)=12.407 E(ANGL)=15.437 | | E(DIHE)=0.000 E(IMPR)=7.675 E(VDW )=10.073 E(ELEC)=6.858 | | E(CDIH)=2.014 E(NOE )=11.920 E(PLAN)=2.365 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61352 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61248 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61204 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61178 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61181 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61175 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61157 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61149 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=1179.698 E(kin)=592.036 temperature=293.379 | | Etotal =587.662 grad(E)=67.224 E(BOND)=213.096 E(ANGL)=414.697 | | E(DIHE)=0.000 E(IMPR)=103.941 E(VDW )=-205.246 E(ELEC)=-127.808 | | E(CDIH)=2.516 E(NOE )=170.887 E(PLAN)=15.579 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61146 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61180 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61137 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.39 A apart NBONDS: found 61144 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61121 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61100 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61117 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61157 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=1161.241 E(kin)=614.029 temperature=304.277 | | Etotal =547.212 grad(E)=66.295 E(BOND)=197.672 E(ANGL)=392.703 | | E(DIHE)=0.000 E(IMPR)=101.191 E(VDW )=-205.968 E(ELEC)=-124.919 | | E(CDIH)=2.005 E(NOE )=168.610 E(PLAN)=15.918 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61176 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61226 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61259 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61294 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61370 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61461 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61487 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=1173.205 E(kin)=602.839 temperature=298.732 | | Etotal =570.367 grad(E)=66.969 E(BOND)=218.458 E(ANGL)=406.479 | | E(DIHE)=0.000 E(IMPR)=98.083 E(VDW )=-201.213 E(ELEC)=-126.290 | | E(CDIH)=0.909 E(NOE )=153.031 E(PLAN)=20.911 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61568 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61624 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61598 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61621 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61667 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61702 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=1185.401 E(kin)=596.248 temperature=295.466 | | Etotal =589.153 grad(E)=69.171 E(BOND)=225.188 E(ANGL)=416.003 | | E(DIHE)=0.000 E(IMPR)=106.481 E(VDW )=-183.916 E(ELEC)=-133.300 | | E(CDIH)=5.449 E(NOE )=138.053 E(PLAN)=15.195 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61748 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61775 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61760 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61705 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61734 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61676 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61643 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=1175.428 E(kin)=584.137 temperature=289.464 | | Etotal =591.291 grad(E)=70.303 E(BOND)=246.396 E(ANGL)=413.673 | | E(DIHE)=0.000 E(IMPR)=94.893 E(VDW )=-190.613 E(ELEC)=-131.229 | | E(CDIH)=5.073 E(NOE )=139.384 E(PLAN)=13.715 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61683 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61682 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61679 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61687 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61611 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61573 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61498 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=1165.536 E(kin)=614.367 temperature=304.445 | | Etotal =551.168 grad(E)=65.818 E(BOND)=214.494 E(ANGL)=393.183 | | E(DIHE)=0.000 E(IMPR)=88.359 E(VDW )=-193.112 E(ELEC)=-133.441 | | E(CDIH)=3.008 E(NOE )=165.356 E(PLAN)=13.320 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -HO2'" and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61481 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61444 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61421 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61476 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61509 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61518 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=1166.067 E(kin)=597.936 temperature=296.302 | | Etotal =568.131 grad(E)=68.168 E(BOND)=234.914 E(ANGL)=404.819 | | E(DIHE)=0.000 E(IMPR)=95.726 E(VDW )=-186.770 E(ELEC)=-136.505 | | E(CDIH)=3.194 E(NOE )=137.312 E(PLAN)=15.442 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61559 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61483 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61490 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61429 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61502 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61433 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61464 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=1177.832 E(kin)=618.579 temperature=306.532 | | Etotal =559.254 grad(E)=67.371 E(BOND)=224.083 E(ANGL)=405.134 | | E(DIHE)=0.000 E(IMPR)=89.296 E(VDW )=-191.311 E(ELEC)=-135.523 | | E(CDIH)=0.712 E(NOE )=150.273 E(PLAN)=16.590 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61448 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61381 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61425 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61469 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61470 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61496 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61515 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=1192.104 E(kin)=596.775 temperature=295.727 | | Etotal =595.329 grad(E)=68.442 E(BOND)=222.587 E(ANGL)=413.162 | | E(DIHE)=0.000 E(IMPR)=107.977 E(VDW )=-184.946 E(ELEC)=-133.980 | | E(CDIH)=3.713 E(NOE )=149.728 E(PLAN)=17.088 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61492 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61495 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61431 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61407 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61371 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61350 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61322 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=1177.085 E(kin)=590.880 temperature=292.806 | | Etotal =586.205 grad(E)=69.583 E(BOND)=239.947 E(ANGL)=400.561 | | E(DIHE)=0.000 E(IMPR)=99.078 E(VDW )=-194.746 E(ELEC)=-125.243 | | E(CDIH)=2.184 E(NOE )=150.075 E(PLAN)=14.349 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1173.616 E(kin)=605.428 temperature=300.015 | | Etotal =568.188 grad(E)=67.364 E(BOND)=228.262 E(ANGL)=398.494 | | E(DIHE)=0.000 E(IMPR)=94.015 E(VDW )=-193.381 E(ELEC)=-131.097 | | E(CDIH)=3.382 E(NOE )=152.704 E(PLAN)=15.809 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=10.206 E(kin)=12.014 temperature=5.953 | | Etotal =15.366 grad(E)=1.370 E(BOND)=10.174 E(ANGL)=13.057 | | E(DIHE)=0.000 E(IMPR)=7.086 E(VDW )=7.828 E(ELEC)=4.656 | | E(CDIH)=1.864 E(NOE )=11.006 E(PLAN)=2.155 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=1171.677 E(kin)=605.148 temperature=299.876 | | Etotal =566.529 grad(E)=65.789 E(BOND)=218.684 E(ANGL)=397.558 | | E(DIHE)=0.000 E(IMPR)=94.014 E(VDW )=-194.309 E(ELEC)=-128.274 | | E(CDIH)=3.739 E(NOE )=158.947 E(PLAN)=16.170 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=20.067 E(kin)=14.143 temperature=7.009 | | Etotal =20.312 grad(E)=1.720 E(BOND)=12.802 E(ANGL)=15.072 | | E(DIHE)=0.000 E(IMPR)=7.580 E(VDW )=9.744 E(ELEC)=6.663 | | E(CDIH)=1.996 E(NOE )=12.099 E(PLAN)=2.337 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61336 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61305 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61303 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61337 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61376 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61413 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61444 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61519 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=1175.153 E(kin)=611.425 temperature=302.987 | | Etotal =563.728 grad(E)=67.407 E(BOND)=222.736 E(ANGL)=423.384 | | E(DIHE)=0.000 E(IMPR)=98.509 E(VDW )=-192.054 E(ELEC)=-145.264 | | E(CDIH)=5.800 E(NOE )=135.011 E(PLAN)=15.607 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61514 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61524 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61497 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61510 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61487 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61466 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=1167.723 E(kin)=611.461 temperature=303.005 | | Etotal =556.263 grad(E)=65.955 E(BOND)=217.261 E(ANGL)=400.714 | | E(DIHE)=0.000 E(IMPR)=88.326 E(VDW )=-170.934 E(ELEC)=-142.371 | | E(CDIH)=3.684 E(NOE )=143.437 E(PLAN)=16.145 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61421 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61415 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61351 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61380 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61423 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61319 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61305 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61287 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=1175.617 E(kin)=614.165 temperature=304.345 | | Etotal =561.452 grad(E)=67.466 E(BOND)=224.703 E(ANGL)=377.139 | | E(DIHE)=0.000 E(IMPR)=94.676 E(VDW )=-187.035 E(ELEC)=-135.647 | | E(CDIH)=3.461 E(NOE )=170.864 E(PLAN)=13.291 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61371 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61354 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61336 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61373 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61336 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61292 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -O5' " only 1.47 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61239 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=1164.181 E(kin)=594.732 temperature=294.715 | | Etotal =569.449 grad(E)=66.489 E(BOND)=226.266 E(ANGL)=412.839 | | E(DIHE)=0.000 E(IMPR)=90.853 E(VDW )=-193.984 E(ELEC)=-133.122 | | E(CDIH)=1.056 E(NOE )=148.452 E(PLAN)=17.090 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61163 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61128 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61066 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61074 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61061 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 60975 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60965 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 60948 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=1180.264 E(kin)=588.846 temperature=291.798 | | Etotal =591.418 grad(E)=68.692 E(BOND)=232.180 E(ANGL)=415.684 | | E(DIHE)=0.000 E(IMPR)=97.364 E(VDW )=-198.732 E(ELEC)=-135.905 | | E(CDIH)=0.971 E(NOE )=163.356 E(PLAN)=16.501 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 60901 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 60849 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60807 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 60792 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 60832 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 60835 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 60873 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 60829 intra-atom interactions NBONDS: found 60799 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=1161.589 E(kin)=585.171 temperature=289.977 | | Etotal =576.418 grad(E)=67.729 E(BOND)=219.910 E(ANGL)=405.523 | | E(DIHE)=0.000 E(IMPR)=97.425 E(VDW )=-210.227 E(ELEC)=-127.908 | | E(CDIH)=3.654 E(NOE )=172.492 E(PLAN)=15.547 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 60768 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 60813 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60841 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60841 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60888 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 60914 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 60951 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 60945 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 60964 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=1188.414 E(kin)=612.981 temperature=303.758 | | Etotal =575.434 grad(E)=67.242 E(BOND)=230.288 E(ANGL)=404.756 | | E(DIHE)=0.000 E(IMPR)=96.845 E(VDW )=-192.866 E(ELEC)=-136.658 | | E(CDIH)=2.551 E(NOE )=152.335 E(PLAN)=18.182 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 60904 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 60869 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 60858 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60877 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 60919 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61095 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61141 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=1156.644 E(kin)=613.194 temperature=303.864 | | Etotal =543.449 grad(E)=66.226 E(BOND)=220.084 E(ANGL)=416.480 | | E(DIHE)=0.000 E(IMPR)=84.346 E(VDW )=-191.227 E(ELEC)=-149.720 | | E(CDIH)=6.005 E(NOE )=138.704 E(PLAN)=18.777 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61252 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61260 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61341 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61384 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61318 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61251 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61252 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61257 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=1176.128 E(kin)=631.887 temperature=313.126 | | Etotal =544.241 grad(E)=65.814 E(BOND)=207.160 E(ANGL)=419.747 | | E(DIHE)=0.000 E(IMPR)=90.938 E(VDW )=-189.250 E(ELEC)=-137.678 | | E(CDIH)=3.978 E(NOE )=136.951 E(PLAN)=12.395 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61303 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61379 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61430 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61425 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61401 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61356 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61294 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=1165.761 E(kin)=589.990 temperature=292.365 | | Etotal =575.770 grad(E)=67.396 E(BOND)=240.795 E(ANGL)=414.037 | | E(DIHE)=0.000 E(IMPR)=85.439 E(VDW )=-190.879 E(ELEC)=-133.490 | | E(CDIH)=5.031 E(NOE )=140.641 E(PLAN)=14.196 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1175.341 E(kin)=605.535 temperature=300.068 | | Etotal =569.806 grad(E)=67.550 E(BOND)=225.517 E(ANGL)=406.955 | | E(DIHE)=0.000 E(IMPR)=92.813 E(VDW )=-190.355 E(ELEC)=-137.352 | | E(CDIH)=3.671 E(NOE )=152.537 E(PLAN)=16.018 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.804 E(kin)=12.694 temperature=6.291 | | Etotal =14.989 grad(E)=1.384 E(BOND)=10.812 E(ANGL)=13.919 | | E(DIHE)=0.000 E(IMPR)=6.807 E(VDW )=7.636 E(ELEC)=5.112 | | E(CDIH)=2.053 E(NOE )=9.776 E(PLAN)=1.980 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=1172.200 E(kin)=605.203 temperature=299.904 | | Etotal =566.997 grad(E)=66.041 E(BOND)=219.660 E(ANGL)=398.900 | | E(DIHE)=0.000 E(IMPR)=93.843 E(VDW )=-193.744 E(ELEC)=-129.571 | | E(CDIH)=3.729 E(NOE )=158.031 E(PLAN)=16.148 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=18.917 E(kin)=13.946 temperature=6.911 | | Etotal =19.674 grad(E)=1.786 E(BOND)=12.763 E(ANGL)=15.271 | | E(DIHE)=0.000 E(IMPR)=7.486 E(VDW )=9.572 E(ELEC)=7.203 | | E(CDIH)=2.004 E(NOE )=12.007 E(PLAN)=2.290 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61183 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61169 intra-atom interactions %atoms "A -9 -URI -O4 " and "A -14 -ADE -H61 " only 1.49 A apart %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61194 intra-atom interactions %atoms "A -9 -URI -O4 " and "A -14 -ADE -H61 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61155 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61173 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61195 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61220 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61236 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=1171.717 E(kin)=624.233 temperature=309.334 | | Etotal =547.484 grad(E)=66.865 E(BOND)=227.622 E(ANGL)=400.762 | | E(DIHE)=0.000 E(IMPR)=98.434 E(VDW )=-196.848 E(ELEC)=-132.089 | | E(CDIH)=1.420 E(NOE )=133.763 E(PLAN)=14.420 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61161 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61096 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61059 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61079 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61067 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61077 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61088 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=1182.684 E(kin)=586.242 temperature=290.508 | | Etotal =596.442 grad(E)=68.637 E(BOND)=249.747 E(ANGL)=409.758 | | E(DIHE)=0.000 E(IMPR)=96.531 E(VDW )=-188.881 E(ELEC)=-135.918 | | E(CDIH)=0.726 E(NOE )=145.454 E(PLAN)=19.026 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61035 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61012 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 60992 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60976 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 60917 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 60896 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 60904 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 60881 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=1183.921 E(kin)=596.580 temperature=295.631 | | Etotal =587.341 grad(E)=69.493 E(BOND)=245.328 E(ANGL)=394.825 | | E(DIHE)=0.000 E(IMPR)=89.844 E(VDW )=-188.072 E(ELEC)=-137.505 | | E(CDIH)=4.187 E(NOE )=157.643 E(PLAN)=21.091 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 60855 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 60843 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 60782 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 60796 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.21 A apart NBONDS: found 60794 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 60868 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 60899 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=1178.793 E(kin)=591.412 temperature=293.070 | | Etotal =587.380 grad(E)=68.383 E(BOND)=231.037 E(ANGL)=423.059 | | E(DIHE)=0.000 E(IMPR)=96.981 E(VDW )=-201.700 E(ELEC)=-134.227 | | E(CDIH)=2.350 E(NOE )=153.608 E(PLAN)=16.272 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61030 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61022 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61032 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61081 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61078 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61134 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=1178.641 E(kin)=599.286 temperature=296.972 | | Etotal =579.354 grad(E)=69.375 E(BOND)=221.751 E(ANGL)=400.311 | | E(DIHE)=0.000 E(IMPR)=93.936 E(VDW )=-179.181 E(ELEC)=-135.287 | | E(CDIH)=3.837 E(NOE )=159.121 E(PLAN)=14.867 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61115 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61196 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61211 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61211 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61221 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61226 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61267 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61246 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=1158.514 E(kin)=611.093 temperature=302.822 | | Etotal =547.421 grad(E)=67.762 E(BOND)=227.093 E(ANGL)=405.550 | | E(DIHE)=0.000 E(IMPR)=90.707 E(VDW )=-189.407 E(ELEC)=-135.760 | | E(CDIH)=5.317 E(NOE )=127.128 E(PLAN)=16.792 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61269 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61293 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61309 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61359 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61415 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61444 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61516 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=1162.609 E(kin)=613.213 temperature=303.873 | | Etotal =549.396 grad(E)=67.745 E(BOND)=228.154 E(ANGL)=382.219 | | E(DIHE)=0.000 E(IMPR)=100.152 E(VDW )=-188.365 E(ELEC)=-140.504 | | E(CDIH)=3.998 E(NOE )=147.825 E(PLAN)=15.916 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61459 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61495 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61452 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61462 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61514 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61533 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61500 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61481 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=1171.239 E(kin)=609.583 temperature=302.074 | | Etotal =561.656 grad(E)=68.703 E(BOND)=229.168 E(ANGL)=405.613 | | E(DIHE)=0.000 E(IMPR)=101.653 E(VDW )=-195.140 E(ELEC)=-141.320 | | E(CDIH)=3.840 E(NOE )=141.334 E(PLAN)=16.508 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61481 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61471 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61473 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61571 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61606 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61670 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61714 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=1173.281 E(kin)=610.642 temperature=302.599 | | Etotal =562.638 grad(E)=69.296 E(BOND)=224.882 E(ANGL)=392.169 | | E(DIHE)=0.000 E(IMPR)=97.833 E(VDW )=-177.777 E(ELEC)=-135.570 | | E(CDIH)=1.561 E(NOE )=145.633 E(PLAN)=13.907 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61712 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61672 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61705 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61714 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61698 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61726 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 61693 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61738 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61727 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=1159.568 E(kin)=599.325 temperature=296.991 | | Etotal =560.243 grad(E)=66.217 E(BOND)=224.161 E(ANGL)=387.713 | | E(DIHE)=0.000 E(IMPR)=85.909 E(VDW )=-195.914 E(ELEC)=-132.492 | | E(CDIH)=1.598 E(NOE )=175.819 E(PLAN)=13.449 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1175.136 E(kin)=605.512 temperature=300.057 | | Etotal =569.624 grad(E)=67.910 E(BOND)=230.367 E(ANGL)=403.744 | | E(DIHE)=0.000 E(IMPR)=92.563 E(VDW )=-191.284 E(ELEC)=-135.782 | | E(CDIH)=3.412 E(NOE )=150.612 E(PLAN)=15.992 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.659 E(kin)=12.680 temperature=6.284 | | Etotal =15.515 grad(E)=1.422 E(BOND)=10.996 E(ANGL)=14.225 | | E(DIHE)=0.000 E(IMPR)=6.443 E(VDW )=7.205 E(ELEC)=3.271 | | E(CDIH)=1.929 E(NOE )=9.693 E(PLAN)=2.163 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=1172.567 E(kin)=605.242 temperature=299.923 | | Etotal =567.326 grad(E)=66.274 E(BOND)=220.999 E(ANGL)=399.506 | | E(DIHE)=0.000 E(IMPR)=93.683 E(VDW )=-193.437 E(ELEC)=-130.347 | | E(CDIH)=3.689 E(NOE )=157.104 E(PLAN)=16.129 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=18.048 E(kin)=13.795 temperature=6.836 | | Etotal =19.223 grad(E)=1.851 E(BOND)=13.045 E(ANGL)=15.229 | | E(DIHE)=0.000 E(IMPR)=7.376 E(VDW )=9.345 E(ELEC)=7.138 | | E(CDIH)=1.998 E(NOE )=11.996 E(PLAN)=2.275 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61713 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61788 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61768 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61804 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61765 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61701 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61649 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61671 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=1163.332 E(kin)=593.801 temperature=294.253 | | Etotal =569.531 grad(E)=69.824 E(BOND)=232.673 E(ANGL)=409.434 | | E(DIHE)=0.000 E(IMPR)=91.925 E(VDW )=-189.322 E(ELEC)=-137.496 | | E(CDIH)=3.233 E(NOE )=146.655 E(PLAN)=12.430 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61637 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61624 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61576 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61595 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61613 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61664 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61711 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=1158.672 E(kin)=585.927 temperature=290.352 | | Etotal =572.744 grad(E)=69.208 E(BOND)=216.950 E(ANGL)=408.581 | | E(DIHE)=0.000 E(IMPR)=102.594 E(VDW )=-201.055 E(ELEC)=-130.667 | | E(CDIH)=0.534 E(NOE )=158.348 E(PLAN)=17.459 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61729 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61828 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61883 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61889 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61869 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61900 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61937 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=1172.984 E(kin)=580.483 temperature=287.654 | | Etotal =592.501 grad(E)=67.327 E(BOND)=233.177 E(ANGL)=417.377 | | E(DIHE)=0.000 E(IMPR)=109.874 E(VDW )=-182.417 E(ELEC)=-137.802 | | E(CDIH)=3.777 E(NOE )=130.139 E(PLAN)=18.376 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61947 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61898 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61836 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61785 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61669 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61625 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61604 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=1162.272 E(kin)=608.826 temperature=301.699 | | Etotal =553.445 grad(E)=66.500 E(BOND)=207.743 E(ANGL)=406.248 | | E(DIHE)=0.000 E(IMPR)=83.259 E(VDW )=-188.728 E(ELEC)=-137.612 | | E(CDIH)=1.227 E(NOE )=159.992 E(PLAN)=21.318 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61647 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61675 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61706 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61848 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62060 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=1165.516 E(kin)=628.552 temperature=311.474 | | Etotal =536.964 grad(E)=66.922 E(BOND)=220.672 E(ANGL)=391.081 | | E(DIHE)=0.000 E(IMPR)=93.364 E(VDW )=-199.666 E(ELEC)=-138.504 | | E(CDIH)=2.990 E(NOE )=152.102 E(PLAN)=14.924 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62036 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62117 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62175 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62191 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62204 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62326 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62341 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=1163.051 E(kin)=610.911 temperature=302.732 | | Etotal =552.141 grad(E)=66.902 E(BOND)=223.134 E(ANGL)=417.468 | | E(DIHE)=0.000 E(IMPR)=88.305 E(VDW )=-194.961 E(ELEC)=-133.563 | | E(CDIH)=3.856 E(NOE )=133.278 E(PLAN)=14.624 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62336 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 62244 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62195 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62210 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62186 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62182 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=1175.852 E(kin)=579.064 temperature=286.951 | | Etotal =596.787 grad(E)=69.549 E(BOND)=239.538 E(ANGL)=402.960 | | E(DIHE)=0.000 E(IMPR)=97.125 E(VDW )=-201.033 E(ELEC)=-127.151 | | E(CDIH)=2.195 E(NOE )=164.959 E(PLAN)=18.195 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62273 intra-atom interactions NBONDS: found 62238 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 62349 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62323 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62340 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62363 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 62291 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=1172.503 E(kin)=621.882 temperature=308.169 | | Etotal =550.621 grad(E)=65.129 E(BOND)=219.965 E(ANGL)=385.116 | | E(DIHE)=0.000 E(IMPR)=97.614 E(VDW )=-186.935 E(ELEC)=-135.254 | | E(CDIH)=4.417 E(NOE )=150.074 E(PLAN)=15.624 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62274 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62225 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62273 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62222 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62235 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 62165 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=1170.986 E(kin)=615.751 temperature=305.130 | | Etotal =555.235 grad(E)=68.195 E(BOND)=237.087 E(ANGL)=382.160 | | E(DIHE)=0.000 E(IMPR)=102.350 E(VDW )=-197.389 E(ELEC)=-142.315 | | E(CDIH)=2.493 E(NOE )=154.313 E(PLAN)=16.536 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62144 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62120 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62058 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62010 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62098 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=1169.762 E(kin)=608.532 temperature=301.553 | | Etotal =561.230 grad(E)=67.818 E(BOND)=216.419 E(ANGL)=406.235 | | E(DIHE)=0.000 E(IMPR)=104.885 E(VDW )=-200.543 E(ELEC)=-131.116 | | E(CDIH)=4.475 E(NOE )=147.325 E(PLAN)=13.548 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1169.571 E(kin)=605.462 temperature=300.032 | | Etotal =564.109 grad(E)=67.241 E(BOND)=225.408 E(ANGL)=400.156 | | E(DIHE)=0.000 E(IMPR)=93.755 E(VDW )=-194.039 E(ELEC)=-133.297 | | E(CDIH)=3.164 E(NOE )=152.833 E(PLAN)=16.130 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.488 E(kin)=12.972 temperature=6.428 | | Etotal =15.041 grad(E)=1.439 E(BOND)=9.938 E(ANGL)=13.390 | | E(DIHE)=0.000 E(IMPR)=7.419 E(VDW )=8.556 E(ELEC)=3.862 | | E(CDIH)=1.689 E(NOE )=10.040 E(PLAN)=2.268 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=1172.234 E(kin)=605.266 temperature=299.935 | | Etotal =566.968 grad(E)=66.382 E(BOND)=221.489 E(ANGL)=399.578 | | E(DIHE)=0.000 E(IMPR)=93.691 E(VDW )=-193.504 E(ELEC)=-130.675 | | E(CDIH)=3.631 E(NOE )=156.629 E(PLAN)=16.129 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=17.275 E(kin)=13.706 temperature=6.792 | | Etotal =18.831 grad(E)=1.835 E(BOND)=12.813 E(ANGL)=15.037 | | E(DIHE)=0.000 E(IMPR)=7.381 E(VDW )=9.262 E(ELEC)=6.914 | | E(CDIH)=1.973 E(NOE )=11.871 E(PLAN)=2.275 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62249 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62403 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62533 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62613 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62637 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=1146.189 E(kin)=607.618 temperature=301.100 | | Etotal =538.571 grad(E)=64.732 E(BOND)=221.677 E(ANGL)=381.891 | | E(DIHE)=0.000 E(IMPR)=95.096 E(VDW )=-179.699 E(ELEC)=-138.549 | | E(CDIH)=0.768 E(NOE )=143.196 E(PLAN)=14.191 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 62698 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62697 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62737 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62772 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=1152.207 E(kin)=616.121 temperature=305.314 | | Etotal =536.086 grad(E)=64.989 E(BOND)=216.323 E(ANGL)=386.096 | | E(DIHE)=0.000 E(IMPR)=90.278 E(VDW )=-198.624 E(ELEC)=-140.920 | | E(CDIH)=1.526 E(NOE )=164.661 E(PLAN)=16.746 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 62849 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62920 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 63021 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 63166 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 63148 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=1176.749 E(kin)=616.919 temperature=305.709 | | Etotal =559.830 grad(E)=67.306 E(BOND)=224.984 E(ANGL)=398.537 | | E(DIHE)=0.000 E(IMPR)=94.623 E(VDW )=-196.217 E(ELEC)=-139.036 | | E(CDIH)=6.089 E(NOE )=151.901 E(PLAN)=18.949 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 63124 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 63058 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 63011 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62977 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62955 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=1178.716 E(kin)=614.895 temperature=304.706 | | Etotal =563.821 grad(E)=66.028 E(BOND)=233.735 E(ANGL)=377.294 | | E(DIHE)=0.000 E(IMPR)=97.456 E(VDW )=-198.350 E(ELEC)=-135.369 | | E(CDIH)=4.022 E(NOE )=167.725 E(PLAN)=17.310 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62924 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62929 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.19 A apart NBONDS: found 62960 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.19 A apart NBONDS: found 62959 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62979 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=1160.949 E(kin)=586.444 temperature=290.607 | | Etotal =574.505 grad(E)=68.368 E(BOND)=236.747 E(ANGL)=403.830 | | E(DIHE)=0.000 E(IMPR)=94.652 E(VDW )=-195.689 E(ELEC)=-137.023 | | E(CDIH)=1.974 E(NOE )=156.119 E(PLAN)=13.897 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62899 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62821 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 62714 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62591 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62530 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62456 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=1179.932 E(kin)=581.899 temperature=288.356 | | Etotal =598.033 grad(E)=70.395 E(BOND)=237.275 E(ANGL)=412.641 | | E(DIHE)=0.000 E(IMPR)=98.348 E(VDW )=-194.157 E(ELEC)=-137.419 | | E(CDIH)=0.357 E(NOE )=166.526 E(PLAN)=14.462 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62360 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 62438 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62502 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62669 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62770 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62825 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62950 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 63054 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=1162.952 E(kin)=602.002 temperature=298.317 | | Etotal =560.950 grad(E)=68.102 E(BOND)=226.628 E(ANGL)=391.440 | | E(DIHE)=0.000 E(IMPR)=96.092 E(VDW )=-191.128 E(ELEC)=-142.649 | | E(CDIH)=2.220 E(NOE )=161.929 E(PLAN)=16.417 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 63138 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 63197 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 63220 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 63147 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 63089 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62920 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=1178.848 E(kin)=578.777 temperature=286.808 | | Etotal =600.071 grad(E)=69.360 E(BOND)=238.841 E(ANGL)=399.823 | | E(DIHE)=0.000 E(IMPR)=104.024 E(VDW )=-191.448 E(ELEC)=-132.100 | | E(CDIH)=4.015 E(NOE )=160.276 E(PLAN)=16.641 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62871 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62897 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62926 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62910 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62913 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62909 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62813 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62789 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=1164.674 E(kin)=609.304 temperature=301.936 | | Etotal =555.370 grad(E)=67.642 E(BOND)=234.886 E(ANGL)=409.560 | | E(DIHE)=0.000 E(IMPR)=91.779 E(VDW )=-206.234 E(ELEC)=-145.224 | | E(CDIH)=3.770 E(NOE )=147.895 E(PLAN)=18.938 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62743 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 62705 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62739 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62766 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62716 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62721 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62651 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62688 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=1165.655 E(kin)=597.234 temperature=295.954 | | Etotal =568.422 grad(E)=67.760 E(BOND)=229.182 E(ANGL)=409.706 | | E(DIHE)=0.000 E(IMPR)=96.142 E(VDW )=-194.230 E(ELEC)=-145.028 | | E(CDIH)=1.804 E(NOE )=153.248 E(PLAN)=17.598 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1167.602 E(kin)=605.500 temperature=300.051 | | Etotal =562.101 grad(E)=67.501 E(BOND)=225.362 E(ANGL)=400.720 | | E(DIHE)=0.000 E(IMPR)=94.383 E(VDW )=-196.313 E(ELEC)=-138.357 | | E(CDIH)=3.676 E(NOE )=156.667 E(PLAN)=15.964 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.003 E(kin)=13.335 temperature=6.608 | | Etotal =15.651 grad(E)=1.395 E(BOND)=10.630 E(ANGL)=14.182 | | E(DIHE)=0.000 E(IMPR)=6.511 E(VDW )=6.487 E(ELEC)=5.422 | | E(CDIH)=1.968 E(NOE )=9.365 E(PLAN)=1.982 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=1171.771 E(kin)=605.290 temperature=299.946 | | Etotal =566.481 grad(E)=66.494 E(BOND)=221.876 E(ANGL)=399.692 | | E(DIHE)=0.000 E(IMPR)=93.760 E(VDW )=-193.785 E(ELEC)=-131.443 | | E(CDIH)=3.636 E(NOE )=156.633 E(PLAN)=16.113 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=16.692 E(kin)=13.669 temperature=6.774 | | Etotal =18.595 grad(E)=1.827 E(BOND)=12.665 E(ANGL)=14.958 | | E(DIHE)=0.000 E(IMPR)=7.302 E(VDW )=9.063 E(ELEC)=7.161 | | E(CDIH)=1.972 E(NOE )=11.645 E(PLAN)=2.248 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62724 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62726 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62652 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62592 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62609 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62521 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 62489 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=1180.247 E(kin)=603.607 temperature=299.112 | | Etotal =576.641 grad(E)=68.230 E(BOND)=215.337 E(ANGL)=413.930 | | E(DIHE)=0.000 E(IMPR)=107.519 E(VDW )=-204.295 E(ELEC)=-125.056 | | E(CDIH)=5.401 E(NOE )=151.597 E(PLAN)=12.207 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 62512 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62489 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 62527 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62514 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62517 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62502 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62418 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=1167.931 E(kin)=605.534 temperature=300.068 | | Etotal =562.397 grad(E)=69.512 E(BOND)=240.219 E(ANGL)=385.325 | | E(DIHE)=0.000 E(IMPR)=98.702 E(VDW )=-195.308 E(ELEC)=-147.147 | | E(CDIH)=5.658 E(NOE )=155.151 E(PLAN)=19.796 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62397 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62364 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62327 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62255 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62237 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62159 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62120 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=1179.022 E(kin)=594.177 temperature=294.440 | | Etotal =584.845 grad(E)=69.373 E(BOND)=234.126 E(ANGL)=412.818 | | E(DIHE)=0.000 E(IMPR)=100.317 E(VDW )=-197.236 E(ELEC)=-143.995 | | E(CDIH)=4.679 E(NOE )=154.300 E(PLAN)=19.835 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62180 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62251 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62266 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62218 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62209 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62164 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62136 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=1159.636 E(kin)=607.325 temperature=300.955 | | Etotal =552.311 grad(E)=66.727 E(BOND)=231.072 E(ANGL)=391.167 | | E(DIHE)=0.000 E(IMPR)=89.266 E(VDW )=-198.747 E(ELEC)=-131.442 | | E(CDIH)=3.532 E(NOE )=148.247 E(PLAN)=19.215 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62058 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62109 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 62135 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62189 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62339 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62433 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=1190.514 E(kin)=598.434 temperature=296.549 | | Etotal =592.080 grad(E)=69.737 E(BOND)=243.728 E(ANGL)=389.575 | | E(DIHE)=0.000 E(IMPR)=110.895 E(VDW )=-192.740 E(ELEC)=-135.680 | | E(CDIH)=3.552 E(NOE )=157.059 E(PLAN)=15.689 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62490 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 62486 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62483 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62436 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62454 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62411 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62281 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62180 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=1174.459 E(kin)=603.387 temperature=299.004 | | Etotal =571.071 grad(E)=67.709 E(BOND)=231.975 E(ANGL)=403.402 | | E(DIHE)=0.000 E(IMPR)=93.151 E(VDW )=-211.342 E(ELEC)=-124.852 | | E(CDIH)=1.602 E(NOE )=163.848 E(PLAN)=13.287 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62064 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61981 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61930 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61945 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61886 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61861 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61871 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=1174.464 E(kin)=609.319 temperature=301.943 | | Etotal =565.145 grad(E)=67.453 E(BOND)=210.957 E(ANGL)=408.513 | | E(DIHE)=0.000 E(IMPR)=116.752 E(VDW )=-204.058 E(ELEC)=-135.854 | | E(CDIH)=1.853 E(NOE )=151.589 E(PLAN)=15.392 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61813 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61758 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61702 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61677 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61630 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61669 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61710 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=1163.215 E(kin)=602.986 temperature=298.805 | | Etotal =560.229 grad(E)=69.663 E(BOND)=215.816 E(ANGL)=414.516 | | E(DIHE)=0.000 E(IMPR)=95.277 E(VDW )=-201.804 E(ELEC)=-136.376 | | E(CDIH)=1.285 E(NOE )=153.661 E(PLAN)=17.853 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61844 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61971 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61983 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61983 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61933 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61962 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 61927 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=1146.872 E(kin)=598.131 temperature=296.399 | | Etotal =548.742 grad(E)=65.827 E(BOND)=206.780 E(ANGL)=419.407 | | E(DIHE)=0.000 E(IMPR)=93.215 E(VDW )=-200.545 E(ELEC)=-128.320 | | E(CDIH)=2.507 E(NOE )=142.653 E(PLAN)=13.044 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61952 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61981 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61930 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61943 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61916 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61883 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=1162.570 E(kin)=621.379 temperature=307.920 | | Etotal =541.191 grad(E)=67.913 E(BOND)=220.514 E(ANGL)=386.527 | | E(DIHE)=0.000 E(IMPR)=93.984 E(VDW )=-191.847 E(ELEC)=-127.334 | | E(CDIH)=2.460 E(NOE )=142.764 E(PLAN)=14.123 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1169.338 E(kin)=605.516 temperature=300.058 | | Etotal =563.822 grad(E)=68.014 E(BOND)=224.940 E(ANGL)=404.439 | | E(DIHE)=0.000 E(IMPR)=94.877 E(VDW )=-200.940 E(ELEC)=-134.671 | | E(CDIH)=3.227 E(NOE )=155.849 E(PLAN)=16.101 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.690 E(kin)=12.713 temperature=6.300 | | Etotal =15.587 grad(E)=1.366 E(BOND)=10.365 E(ANGL)=12.825 | | E(DIHE)=0.000 E(IMPR)=6.909 E(VDW )=6.936 E(ELEC)=7.097 | | E(CDIH)=1.655 E(NOE )=9.578 E(PLAN)=2.504 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=1171.550 E(kin)=605.310 temperature=299.957 | | Etotal =566.240 grad(E)=66.632 E(BOND)=222.155 E(ANGL)=400.124 | | E(DIHE)=0.000 E(IMPR)=93.861 E(VDW )=-194.435 E(ELEC)=-131.737 | | E(CDIH)=3.598 E(NOE )=156.562 E(PLAN)=16.112 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=16.196 E(kin)=13.585 temperature=6.732 | | Etotal =18.358 grad(E)=1.842 E(BOND)=12.504 E(ANGL)=14.839 | | E(DIHE)=0.000 E(IMPR)=7.274 E(VDW )=9.125 E(ELEC)=7.215 | | E(CDIH)=1.949 E(NOE )=11.474 E(PLAN)=2.272 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61872 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61887 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61927 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61955 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62014 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62033 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=1182.328 E(kin)=614.071 temperature=304.298 | | Etotal =568.257 grad(E)=67.879 E(BOND)=218.853 E(ANGL)=403.991 | | E(DIHE)=0.000 E(IMPR)=97.815 E(VDW )=-200.131 E(ELEC)=-129.125 | | E(CDIH)=1.077 E(NOE )=158.699 E(PLAN)=17.077 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62022 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62015 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62009 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61972 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61912 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61799 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61784 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=1170.406 E(kin)=604.972 temperature=299.789 | | Etotal =565.434 grad(E)=68.010 E(BOND)=237.033 E(ANGL)=411.109 | | E(DIHE)=0.000 E(IMPR)=98.867 E(VDW )=-206.259 E(ELEC)=-131.184 | | E(CDIH)=0.620 E(NOE )=140.025 E(PLAN)=15.223 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61733 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61693 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61686 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61670 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61713 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61794 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61831 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61864 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61931 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=1163.116 E(kin)=609.695 temperature=302.129 | | Etotal =553.421 grad(E)=69.898 E(BOND)=228.879 E(ANGL)=410.861 | | E(DIHE)=0.000 E(IMPR)=86.622 E(VDW )=-203.270 E(ELEC)=-136.898 | | E(CDIH)=3.744 E(NOE )=147.900 E(PLAN)=15.584 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61984 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61984 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61946 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62019 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62015 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62017 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62073 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62014 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=1155.498 E(kin)=602.170 temperature=298.401 | | Etotal =553.328 grad(E)=67.380 E(BOND)=217.764 E(ANGL)=407.624 | | E(DIHE)=0.000 E(IMPR)=89.217 E(VDW )=-196.329 E(ELEC)=-129.469 | | E(CDIH)=2.516 E(NOE )=148.950 E(PLAN)=13.054 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62008 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 62006 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61997 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61997 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62069 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62040 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 62049 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62057 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62029 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=1159.706 E(kin)=629.461 temperature=311.924 | | Etotal =530.245 grad(E)=64.197 E(BOND)=215.498 E(ANGL)=385.551 | | E(DIHE)=0.000 E(IMPR)=96.099 E(VDW )=-206.233 E(ELEC)=-132.176 | | E(CDIH)=1.346 E(NOE )=155.690 E(PLAN)=14.469 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62042 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 62025 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62012 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62051 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62033 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 62027 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 62028 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=1171.978 E(kin)=617.021 temperature=305.760 | | Etotal =554.956 grad(E)=67.950 E(BOND)=223.097 E(ANGL)=417.249 | | E(DIHE)=0.000 E(IMPR)=80.950 E(VDW )=-192.709 E(ELEC)=-128.527 | | E(CDIH)=2.075 E(NOE )=137.092 E(PLAN)=15.729 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62000 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62001 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62038 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62064 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62129 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62213 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62215 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62251 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=1186.293 E(kin)=628.162 temperature=311.281 | | Etotal =558.131 grad(E)=67.262 E(BOND)=221.419 E(ANGL)=399.439 | | E(DIHE)=0.000 E(IMPR)=98.451 E(VDW )=-187.326 E(ELEC)=-143.616 | | E(CDIH)=3.780 E(NOE )=146.666 E(PLAN)=19.319 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 62210 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62194 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.37 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62175 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62173 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62154 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62142 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 62106 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62070 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 62053 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.41 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61979 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=1177.629 E(kin)=612.389 temperature=303.465 | | Etotal =565.240 grad(E)=64.877 E(BOND)=225.339 E(ANGL)=419.278 | | E(DIHE)=0.000 E(IMPR)=88.105 E(VDW )=-198.434 E(ELEC)=-135.053 | | E(CDIH)=4.981 E(NOE )=145.065 E(PLAN)=15.959 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61954 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61884 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61875 intra-atom interactions %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61899 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61912 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61948 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62007 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62034 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=1168.554 E(kin)=594.521 temperature=294.610 | | Etotal =574.033 grad(E)=67.922 E(BOND)=237.570 E(ANGL)=394.060 | | E(DIHE)=0.000 E(IMPR)=102.641 E(VDW )=-190.449 E(ELEC)=-130.998 | | E(CDIH)=2.454 E(NOE )=142.324 E(PLAN)=16.430 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62118 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 62091 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 62103 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62209 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.22 A apart NBONDS: found 62231 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62211 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 62177 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62158 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=1165.700 E(kin)=591.136 temperature=292.933 | | Etotal =574.565 grad(E)=69.614 E(BOND)=231.838 E(ANGL)=408.527 | | E(DIHE)=0.000 E(IMPR)=88.509 E(VDW )=-191.059 E(ELEC)=-136.073 | | E(CDIH)=4.620 E(NOE )=154.136 E(PLAN)=14.067 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1171.160 E(kin)=605.462 temperature=300.032 | | Etotal =565.698 grad(E)=68.099 E(BOND)=225.040 E(ANGL)=404.610 | | E(DIHE)=0.000 E(IMPR)=94.145 E(VDW )=-194.597 E(ELEC)=-133.139 | | E(CDIH)=3.074 E(NOE )=150.579 E(PLAN)=15.985 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.927 E(kin)=12.452 temperature=6.171 | | Etotal =14.932 grad(E)=1.412 E(BOND)=10.446 E(ANGL)=12.405 | | E(DIHE)=0.000 E(IMPR)=6.841 E(VDW )=7.595 E(ELEC)=5.034 | | E(CDIH)=1.614 E(NOE )=8.779 E(PLAN)=2.111 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=1171.517 E(kin)=605.323 temperature=299.963 | | Etotal =566.195 grad(E)=66.754 E(BOND)=222.395 E(ANGL)=400.498 | | E(DIHE)=0.000 E(IMPR)=93.885 E(VDW )=-194.448 E(ELEC)=-131.854 | | E(CDIH)=3.555 E(NOE )=156.063 E(PLAN)=16.101 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=15.720 E(kin)=13.495 temperature=6.687 | | Etotal =18.098 grad(E)=1.855 E(BOND)=12.372 E(ANGL)=14.704 | | E(DIHE)=0.000 E(IMPR)=7.239 E(VDW )=9.008 E(ELEC)=7.069 | | E(CDIH)=1.929 E(NOE )=11.395 E(PLAN)=2.259 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart %atoms "A -12 -URI -HO2'" and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 62118 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 62097 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 62055 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61965 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61979 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 62011 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61965 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=1178.925 E(kin)=598.509 temperature=296.586 | | Etotal =580.416 grad(E)=68.413 E(BOND)=226.994 E(ANGL)=414.579 | | E(DIHE)=0.000 E(IMPR)=92.171 E(VDW )=-201.103 E(ELEC)=-130.955 | | E(CDIH)=3.641 E(NOE )=158.083 E(PLAN)=17.007 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61980 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61989 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61960 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61990 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61878 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61876 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61855 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=1171.308 E(kin)=610.798 temperature=302.676 | | Etotal =560.509 grad(E)=67.513 E(BOND)=219.242 E(ANGL)=392.914 | | E(DIHE)=0.000 E(IMPR)=91.630 E(VDW )=-172.430 E(ELEC)=-132.481 | | E(CDIH)=2.359 E(NOE )=139.842 E(PLAN)=19.434 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61803 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61720 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61671 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61661 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61539 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61467 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61431 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=1177.236 E(kin)=586.394 temperature=290.583 | | Etotal =590.843 grad(E)=70.220 E(BOND)=243.536 E(ANGL)=429.483 | | E(DIHE)=0.000 E(IMPR)=87.144 E(VDW )=-191.491 E(ELEC)=-139.683 | | E(CDIH)=1.780 E(NOE )=143.709 E(PLAN)=16.364 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61381 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61326 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61331 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61287 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61238 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61256 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61197 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61216 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=1175.141 E(kin)=613.793 temperature=304.160 | | Etotal =561.348 grad(E)=66.515 E(BOND)=217.332 E(ANGL)=414.299 | | E(DIHE)=0.000 E(IMPR)=93.156 E(VDW )=-191.185 E(ELEC)=-132.866 | | E(CDIH)=2.838 E(NOE )=139.309 E(PLAN)=18.465 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61196 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61171 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61195 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61207 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61298 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61371 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61546 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=1176.190 E(kin)=603.343 temperature=298.982 | | Etotal =572.847 grad(E)=68.105 E(BOND)=232.707 E(ANGL)=391.986 | | E(DIHE)=0.000 E(IMPR)=101.370 E(VDW )=-195.501 E(ELEC)=-129.960 | | E(CDIH)=7.538 E(NOE )=153.458 E(PLAN)=11.248 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61536 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61596 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61566 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -14 -ADE -H62 " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61553 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -14 -ADE -H62 " only 1.39 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61508 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61385 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=1189.005 E(kin)=604.485 temperature=299.548 | | Etotal =584.519 grad(E)=68.057 E(BOND)=215.605 E(ANGL)=407.879 | | E(DIHE)=0.000 E(IMPR)=98.827 E(VDW )=-198.612 E(ELEC)=-123.733 | | E(CDIH)=2.482 E(NOE )=164.696 E(PLAN)=17.376 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61357 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61360 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -14 -ADE -H62 " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61307 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61316 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61319 intra-atom interactions %atoms "A -8 -CYT -O2 " and "A -14 -ADE -H62 " only 1.40 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61355 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61401 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61386 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=1181.228 E(kin)=589.252 temperature=291.999 | | Etotal =591.976 grad(E)=70.490 E(BOND)=241.682 E(ANGL)=405.477 | | E(DIHE)=0.000 E(IMPR)=103.146 E(VDW )=-196.014 E(ELEC)=-136.040 | | E(CDIH)=2.847 E(NOE )=152.852 E(PLAN)=18.027 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61437 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61397 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61361 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61366 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61258 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61242 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61185 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61144 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=1187.003 E(kin)=581.648 temperature=288.231 | | Etotal =605.355 grad(E)=69.358 E(BOND)=228.070 E(ANGL)=434.904 | | E(DIHE)=0.000 E(IMPR)=98.408 E(VDW )=-190.039 E(ELEC)=-124.088 | | E(CDIH)=2.655 E(NOE )=140.415 E(PLAN)=15.029 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61114 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61056 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61011 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61029 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 60969 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61033 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61086 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61084 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=1181.520 E(kin)=587.671 temperature=291.216 | | Etotal =593.849 grad(E)=70.630 E(BOND)=224.627 E(ANGL)=413.096 | | E(DIHE)=0.000 E(IMPR)=104.051 E(VDW )=-202.612 E(ELEC)=-123.512 | | E(CDIH)=1.932 E(NOE )=163.063 E(PLAN)=13.203 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart %atoms "A -13 -ADE -HO2'" and "A -14 -ADE -H5' " only 1.45 A apart NBONDS: found 61165 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61176 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61209 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61209 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61233 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61235 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61235 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61190 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=1170.072 E(kin)=594.291 temperature=294.496 | | Etotal =575.781 grad(E)=68.452 E(BOND)=232.083 E(ANGL)=398.817 | | E(DIHE)=0.000 E(IMPR)=94.018 E(VDW )=-189.408 E(ELEC)=-133.534 | | E(CDIH)=2.024 E(NOE )=161.207 E(PLAN)=10.575 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1177.732 E(kin)=605.477 temperature=300.039 | | Etotal =572.255 grad(E)=68.444 E(BOND)=226.591 E(ANGL)=407.784 | | E(DIHE)=0.000 E(IMPR)=93.467 E(VDW )=-195.333 E(ELEC)=-129.384 | | E(CDIH)=3.153 E(NOE )=150.392 E(PLAN)=15.585 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.233 E(kin)=12.993 temperature=6.438 | | Etotal =14.919 grad(E)=1.458 E(BOND)=11.065 E(ANGL)=12.934 | | E(DIHE)=0.000 E(IMPR)=6.334 E(VDW )=7.646 E(ELEC)=4.241 | | E(CDIH)=1.674 E(NOE )=9.201 E(PLAN)=2.077 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=1171.995 E(kin)=605.335 temperature=299.969 | | Etotal =566.661 grad(E)=66.884 E(BOND)=222.718 E(ANGL)=401.058 | | E(DIHE)=0.000 E(IMPR)=93.853 E(VDW )=-194.516 E(ELEC)=-131.664 | | E(CDIH)=3.524 E(NOE )=155.627 E(PLAN)=16.061 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=15.364 E(kin)=13.457 temperature=6.668 | | Etotal =17.946 grad(E)=1.882 E(BOND)=12.327 E(ANGL)=14.705 | | E(DIHE)=0.000 E(IMPR)=7.175 E(VDW )=8.913 E(ELEC)=6.925 | | E(CDIH)=1.914 E(NOE )=11.343 E(PLAN)=2.250 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61132 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61155 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.21 A apart NBONDS: found 61176 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.21 A apart NBONDS: found 61153 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61150 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61157 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61129 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61103 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61113 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=1175.415 E(kin)=601.246 temperature=297.943 | | Etotal =574.169 grad(E)=66.354 E(BOND)=226.794 E(ANGL)=404.634 | | E(DIHE)=0.000 E(IMPR)=91.800 E(VDW )=-188.830 E(ELEC)=-138.470 | | E(CDIH)=4.357 E(NOE )=155.802 E(PLAN)=18.084 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61047 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 60962 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61009 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61017 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 60996 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61024 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61111 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -H2 " and "A -13 -ADE -O5' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61100 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=1177.806 E(kin)=620.569 temperature=307.518 | | Etotal =557.237 grad(E)=69.610 E(BOND)=225.963 E(ANGL)=407.465 | | E(DIHE)=0.000 E(IMPR)=94.346 E(VDW )=-193.982 E(ELEC)=-134.983 | | E(CDIH)=3.954 E(NOE )=134.172 E(PLAN)=20.302 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61167 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61200 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61155 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61166 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.49 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61160 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61181 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61116 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61076 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61078 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=1172.939 E(kin)=605.493 temperature=300.047 | | Etotal =567.446 grad(E)=66.524 E(BOND)=227.967 E(ANGL)=395.581 | | E(DIHE)=0.000 E(IMPR)=82.795 E(VDW )=-187.798 E(ELEC)=-134.403 | | E(CDIH)=2.938 E(NOE )=163.977 E(PLAN)=16.388 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61098 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61090 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.45 A apart NBONDS: found 61065 intra-atom interactions NBONDS: found 61044 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61086 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61016 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61032 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61072 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61063 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=1174.444 E(kin)=618.730 temperature=306.607 | | Etotal =555.713 grad(E)=67.607 E(BOND)=211.534 E(ANGL)=426.644 | | E(DIHE)=0.000 E(IMPR)=89.864 E(VDW )=-204.629 E(ELEC)=-131.304 | | E(CDIH)=2.800 E(NOE )=148.694 E(PLAN)=12.110 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61063 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61181 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61180 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61147 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61229 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61242 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61252 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61318 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61319 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=1187.860 E(kin)=586.609 temperature=290.689 | | Etotal =601.251 grad(E)=72.660 E(BOND)=215.020 E(ANGL)=411.168 | | E(DIHE)=0.000 E(IMPR)=99.892 E(VDW )=-178.709 E(ELEC)=-127.802 | | E(CDIH)=5.555 E(NOE )=162.992 E(PLAN)=13.135 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61317 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61283 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61267 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61316 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61308 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61340 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61287 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=1179.801 E(kin)=616.884 temperature=305.692 | | Etotal =562.917 grad(E)=67.953 E(BOND)=226.204 E(ANGL)=397.320 | | E(DIHE)=0.000 E(IMPR)=93.112 E(VDW )=-188.091 E(ELEC)=-134.493 | | E(CDIH)=4.146 E(NOE )=147.326 E(PLAN)=17.393 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61288 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61253 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61269 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61288 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61331 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61393 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61529 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=1187.766 E(kin)=620.134 temperature=307.302 | | Etotal =567.632 grad(E)=69.643 E(BOND)=229.258 E(ANGL)=402.113 | | E(DIHE)=0.000 E(IMPR)=91.397 E(VDW )=-196.225 E(ELEC)=-137.276 | | E(CDIH)=1.333 E(NOE )=163.502 E(PLAN)=13.530 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61501 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61582 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61608 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61625 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61633 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61621 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61600 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61539 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=1183.521 E(kin)=604.363 temperature=299.487 | | Etotal =579.158 grad(E)=69.479 E(BOND)=234.083 E(ANGL)=415.734 | | E(DIHE)=0.000 E(IMPR)=91.930 E(VDW )=-187.691 E(ELEC)=-129.297 | | E(CDIH)=2.636 E(NOE )=134.197 E(PLAN)=17.566 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61530 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61532 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61531 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61567 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61558 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61575 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61574 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=1166.082 E(kin)=605.122 temperature=299.863 | | Etotal =560.960 grad(E)=69.191 E(BOND)=226.098 E(ANGL)=385.162 | | E(DIHE)=0.000 E(IMPR)=107.540 E(VDW )=-200.057 E(ELEC)=-143.642 | | E(CDIH)=3.402 E(NOE )=167.457 E(PLAN)=15.000 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61584 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61631 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61616 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.26 A apart NBONDS: found 61554 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61538 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.42 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61443 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61419 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=1165.390 E(kin)=606.755 temperature=300.672 | | Etotal =558.635 grad(E)=69.268 E(BOND)=231.780 E(ANGL)=384.444 | | E(DIHE)=0.000 E(IMPR)=98.251 E(VDW )=-191.665 E(ELEC)=-136.069 | | E(CDIH)=1.853 E(NOE )=153.825 E(PLAN)=16.215 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1177.727 E(kin)=605.500 temperature=300.051 | | Etotal =572.226 grad(E)=68.962 E(BOND)=224.305 E(ANGL)=409.863 | | E(DIHE)=0.000 E(IMPR)=94.618 E(VDW )=-192.039 E(ELEC)=-135.413 | | E(CDIH)=3.820 E(NOE )=150.951 E(PLAN)=16.122 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.102 E(kin)=12.521 temperature=6.204 | | Etotal =14.471 grad(E)=1.455 E(BOND)=10.609 E(ANGL)=14.082 | | E(DIHE)=0.000 E(IMPR)=7.464 E(VDW )=8.507 E(ELEC)=4.754 | | E(CDIH)=2.013 E(NOE )=9.812 E(PLAN)=2.053 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=1172.405 E(kin)=605.347 temperature=299.975 | | Etotal =567.058 grad(E)=67.033 E(BOND)=222.831 E(ANGL)=401.687 | | E(DIHE)=0.000 E(IMPR)=93.908 E(VDW )=-194.340 E(ELEC)=-131.932 | | E(CDIH)=3.545 E(NOE )=155.293 E(PLAN)=16.066 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=15.035 E(kin)=13.392 temperature=6.636 | | Etotal =17.779 grad(E)=1.931 E(BOND)=12.219 E(ANGL)=14.835 | | E(DIHE)=0.000 E(IMPR)=7.198 E(VDW )=8.908 E(ELEC)=6.861 | | E(CDIH)=1.922 E(NOE )=11.304 E(PLAN)=2.237 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.44 A apart NBONDS: found 61393 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61337 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61354 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61451 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.43 A apart NBONDS: found 61414 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.48 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61443 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61393 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=1175.124 E(kin)=606.024 temperature=300.310 | | Etotal =569.100 grad(E)=69.685 E(BOND)=232.371 E(ANGL)=412.011 | | E(DIHE)=0.000 E(IMPR)=100.208 E(VDW )=-194.324 E(ELEC)=-137.388 | | E(CDIH)=0.716 E(NOE )=140.369 E(PLAN)=15.138 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61398 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61341 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61331 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.43 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61276 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61232 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61197 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61245 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.46 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61289 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=1178.022 E(kin)=626.457 temperature=310.436 | | Etotal =551.566 grad(E)=67.305 E(BOND)=223.482 E(ANGL)=387.527 | | E(DIHE)=0.000 E(IMPR)=91.820 E(VDW )=-188.334 E(ELEC)=-129.045 | | E(CDIH)=2.721 E(NOE )=143.801 E(PLAN)=19.594 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61315 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61410 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61433 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61440 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61494 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61527 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61539 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.27 A apart NBONDS: found 61531 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61514 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=1159.588 E(kin)=585.137 temperature=289.960 | | Etotal =574.451 grad(E)=70.855 E(BOND)=232.837 E(ANGL)=405.848 | | E(DIHE)=0.000 E(IMPR)=95.945 E(VDW )=-191.839 E(ELEC)=-135.157 | | E(CDIH)=1.571 E(NOE )=149.943 E(PLAN)=15.305 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61522 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61504 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61430 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.49 A apart NBONDS: found 61452 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61398 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=1164.943 E(kin)=607.363 temperature=300.974 | | Etotal =557.580 grad(E)=66.326 E(BOND)=222.172 E(ANGL)=394.044 | | E(DIHE)=0.000 E(IMPR)=98.460 E(VDW )=-184.587 E(ELEC)=-138.085 | | E(CDIH)=0.812 E(NOE )=153.302 E(PLAN)=11.462 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61364 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61372 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61340 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61344 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61360 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61348 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61368 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=1181.228 E(kin)=583.696 temperature=289.246 | | Etotal =597.532 grad(E)=67.483 E(BOND)=243.502 E(ANGL)=398.522 | | E(DIHE)=0.000 E(IMPR)=100.391 E(VDW )=-183.830 E(ELEC)=-129.436 | | E(CDIH)=2.078 E(NOE )=150.455 E(PLAN)=15.851 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61245 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61221 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61222 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61240 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61190 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61171 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=1188.600 E(kin)=619.799 temperature=307.136 | | Etotal =568.801 grad(E)=68.033 E(BOND)=219.222 E(ANGL)=380.718 | | E(DIHE)=0.000 E(IMPR)=92.074 E(VDW )=-181.635 E(ELEC)=-132.394 | | E(CDIH)=1.615 E(NOE )=168.857 E(PLAN)=20.346 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61176 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61164 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61163 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61287 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61338 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=1182.300 E(kin)=613.432 temperature=303.981 | | Etotal =568.868 grad(E)=68.778 E(BOND)=254.649 E(ANGL)=385.202 | | E(DIHE)=0.000 E(IMPR)=84.449 E(VDW )=-193.355 E(ELEC)=-138.415 | | E(CDIH)=3.317 E(NOE )=155.070 E(PLAN)=17.951 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61333 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61399 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61350 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61250 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61187 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61166 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61117 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=1162.289 E(kin)=591.549 temperature=293.137 | | Etotal =570.740 grad(E)=68.732 E(BOND)=233.218 E(ANGL)=398.153 | | E(DIHE)=0.000 E(IMPR)=88.910 E(VDW )=-182.668 E(ELEC)=-129.947 | | E(CDIH)=2.808 E(NOE )=147.799 E(PLAN)=12.468 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61103 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61065 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61073 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.46 A apart NBONDS: found 61102 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61118 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61183 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=1181.947 E(kin)=616.494 temperature=305.499 | | Etotal =565.453 grad(E)=68.085 E(BOND)=225.823 E(ANGL)=415.441 | | E(DIHE)=0.000 E(IMPR)=92.882 E(VDW )=-201.761 E(ELEC)=-126.467 | | E(CDIH)=1.917 E(NOE )=143.514 E(PLAN)=14.103 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61344 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61427 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61466 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61457 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61403 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61380 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=1172.554 E(kin)=604.565 temperature=299.587 | | Etotal =567.989 grad(E)=69.372 E(BOND)=229.599 E(ANGL)=397.476 | | E(DIHE)=0.000 E(IMPR)=92.111 E(VDW )=-182.044 E(ELEC)=-130.858 | | E(CDIH)=4.496 E(NOE )=142.788 E(PLAN)=14.422 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1174.582 E(kin)=605.471 temperature=300.036 | | Etotal =569.111 grad(E)=68.475 E(BOND)=229.218 E(ANGL)=401.085 | | E(DIHE)=0.000 E(IMPR)=95.244 E(VDW )=-192.449 E(ELEC)=-132.903 | | E(CDIH)=3.148 E(NOE )=150.025 E(PLAN)=15.743 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.169 E(kin)=12.708 temperature=6.297 | | Etotal =15.232 grad(E)=1.446 E(BOND)=10.439 E(ANGL)=13.191 | | E(DIHE)=0.000 E(IMPR)=6.514 E(VDW )=6.765 E(ELEC)=5.877 | | E(CDIH)=1.695 E(NOE )=8.782 E(PLAN)=2.190 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=1172.550 E(kin)=605.355 temperature=299.979 | | Etotal =567.195 grad(E)=67.129 E(BOND)=223.257 E(ANGL)=401.647 | | E(DIHE)=0.000 E(IMPR)=93.997 E(VDW )=-194.214 E(ELEC)=-131.996 | | E(CDIH)=3.518 E(NOE )=154.942 E(PLAN)=16.044 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=14.727 E(kin)=13.348 temperature=6.614 | | Etotal =17.628 grad(E)=1.936 E(BOND)=12.213 E(ANGL)=14.732 | | E(DIHE)=0.000 E(IMPR)=7.162 E(VDW )=8.794 E(ELEC)=6.804 | | E(CDIH)=1.911 E(NOE )=11.231 E(PLAN)=2.235 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.48 A apart NBONDS: found 61339 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61268 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.21 A apart NBONDS: found 61206 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61079 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 60999 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.25 A apart NBONDS: found 61007 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=1181.543 E(kin)=603.716 temperature=299.167 | | Etotal =577.827 grad(E)=68.435 E(BOND)=231.070 E(ANGL)=396.128 | | E(DIHE)=0.000 E(IMPR)=94.630 E(VDW )=-192.485 E(ELEC)=-129.571 | | E(CDIH)=1.776 E(NOE )=156.342 E(PLAN)=19.936 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61016 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61041 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.39 A apart NBONDS: found 61046 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61040 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61026 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 60999 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=1191.247 E(kin)=581.930 temperature=288.371 | | Etotal =609.316 grad(E)=72.547 E(BOND)=240.721 E(ANGL)=404.965 | | E(DIHE)=0.000 E(IMPR)=102.090 E(VDW )=-207.211 E(ELEC)=-124.088 | | E(CDIH)=1.926 E(NOE )=173.344 E(PLAN)=17.570 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 60942 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 60975 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61040 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61103 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61158 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61098 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61130 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=1192.672 E(kin)=600.702 temperature=297.673 | | Etotal =591.969 grad(E)=69.970 E(BOND)=250.605 E(ANGL)=394.447 | | E(DIHE)=0.000 E(IMPR)=93.514 E(VDW )=-191.378 E(ELEC)=-130.444 | | E(CDIH)=5.334 E(NOE )=152.219 E(PLAN)=17.674 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 61186 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.45 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61238 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61223 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61262 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61264 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.47 A apart NBONDS: found 61303 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61383 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=1192.748 E(kin)=594.201 temperature=294.451 | | Etotal =598.547 grad(E)=68.236 E(BOND)=243.371 E(ANGL)=409.334 | | E(DIHE)=0.000 E(IMPR)=93.896 E(VDW )=-202.654 E(ELEC)=-122.884 | | E(CDIH)=2.952 E(NOE )=160.482 E(PLAN)=14.049 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61420 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61473 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61420 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61468 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61514 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.44 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61461 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61438 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=1189.352 E(kin)=604.726 temperature=299.667 | | Etotal =584.626 grad(E)=69.763 E(BOND)=242.343 E(ANGL)=375.422 | | E(DIHE)=0.000 E(IMPR)=105.461 E(VDW )=-193.241 E(ELEC)=-125.228 | | E(CDIH)=1.811 E(NOE )=161.425 E(PLAN)=16.633 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61400 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61334 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61334 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61308 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.21 A apart NBONDS: found 61312 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61236 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61246 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61277 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=1180.985 E(kin)=603.247 temperature=298.934 | | Etotal =577.738 grad(E)=68.722 E(BOND)=240.663 E(ANGL)=404.257 | | E(DIHE)=0.000 E(IMPR)=73.749 E(VDW )=-188.836 E(ELEC)=-127.197 | | E(CDIH)=2.267 E(NOE )=153.932 E(PLAN)=18.902 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61351 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.29 A apart NBONDS: found 61320 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61382 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61483 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61611 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61588 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=1163.055 E(kin)=603.315 temperature=298.968 | | Etotal =559.739 grad(E)=66.536 E(BOND)=229.423 E(ANGL)=394.930 | | E(DIHE)=0.000 E(IMPR)=87.551 E(VDW )=-193.042 E(ELEC)=-133.202 | | E(CDIH)=3.370 E(NOE )=155.656 E(PLAN)=15.054 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61593 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61653 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61621 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.23 A apart NBONDS: found 61598 intra-atom interactions %atoms "A -10 -CYT -O2' " and "A -11 -ADE -H3' " only 1.47 A apart %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61519 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.41 A apart NBONDS: found 61551 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=1169.905 E(kin)=634.575 temperature=314.459 | | Etotal =535.329 grad(E)=68.163 E(BOND)=221.230 E(ANGL)=377.104 | | E(DIHE)=0.000 E(IMPR)=94.998 E(VDW )=-188.899 E(ELEC)=-122.526 | | E(CDIH)=2.152 E(NOE )=133.783 E(PLAN)=17.487 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.38 A apart NBONDS: found 61507 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61467 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.35 A apart NBONDS: found 61478 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61463 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 61511 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.28 A apart NBONDS: found 61520 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=1176.640 E(kin)=576.201 temperature=285.532 | | Etotal =600.439 grad(E)=70.719 E(BOND)=237.375 E(ANGL)=415.500 | | E(DIHE)=0.000 E(IMPR)=91.234 E(VDW )=-203.268 E(ELEC)=-130.689 | | E(CDIH)=1.198 E(NOE )=178.386 E(PLAN)=10.701 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.34 A apart NBONDS: found 61448 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.42 A apart NBONDS: found 61487 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.37 A apart NBONDS: found 61521 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.31 A apart NBONDS: found 61586 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.24 A apart NBONDS: found 61656 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.36 A apart NBONDS: found 61702 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.40 A apart NBONDS: found 61732 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=1157.762 E(kin)=590.365 temperature=292.551 | | Etotal =567.397 grad(E)=66.790 E(BOND)=223.081 E(ANGL)=411.978 | | E(DIHE)=0.000 E(IMPR)=96.793 E(VDW )=-184.907 E(ELEC)=-140.551 | | E(CDIH)=0.678 E(NOE )=143.034 E(PLAN)=17.292 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=1179.406 E(kin)=605.528 temperature=300.065 | | Etotal =573.878 grad(E)=68.626 E(BOND)=232.520 E(ANGL)=397.350 | | E(DIHE)=0.000 E(IMPR)=94.961 E(VDW )=-194.312 E(ELEC)=-128.827 | | E(CDIH)=3.089 E(NOE )=153.319 E(PLAN)=15.777 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.385 E(kin)=12.675 temperature=6.281 | | Etotal =15.399 grad(E)=1.395 E(BOND)=10.366 E(ANGL)=12.329 | | E(DIHE)=0.000 E(IMPR)=6.500 E(VDW )=7.633 E(ELEC)=4.569 | | E(CDIH)=1.579 E(NOE )=10.037 E(PLAN)=2.131 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=1172.979 E(kin)=605.366 temperature=299.984 | | Etotal =567.613 grad(E)=67.222 E(BOND)=223.836 E(ANGL)=401.378 | | E(DIHE)=0.000 E(IMPR)=94.057 E(VDW )=-194.220 E(ELEC)=-131.798 | | E(CDIH)=3.492 E(NOE )=154.840 E(PLAN)=16.027 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=14.546 E(kin)=13.307 temperature=6.594 | | Etotal =17.571 grad(E)=1.941 E(BOND)=12.312 E(ANGL)=14.631 | | E(DIHE)=0.000 E(IMPR)=7.127 E(VDW )=8.726 E(ELEC)=6.730 | | E(CDIH)=1.894 E(NOE )=11.167 E(PLAN)=2.230 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.08737 0.00469 0.04518 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 08:03:09 created by user: READC: reading file= 1 ISTART= 200 READC: 677 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 20000 SKIP= 200 STOP= 40000 READC: TIMEstep= 0.00050000 ps header= CORD READC: complete. 101 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR>close refine.tra end ! disposition=delete doesn't work X-PLOR> X-PLOR>! Final minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62046 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62048 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.30 A apart NBONDS: found 62028 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =689.104 grad(E)=22.628 E(BOND)=57.974 E(ANGL)=793.945 | | E(DIHE)=0.000 E(IMPR)=20.819 E(VDW )=-159.442 E(ELEC)=-140.865 | | E(CDIH)=0.517 E(NOE )=101.818 E(PLAN)=14.339 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.32 A apart NBONDS: found 62007 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =347.906 grad(E)=22.015 E(BOND)=43.903 E(ANGL)=484.757 | | E(DIHE)=0.000 E(IMPR)=22.514 E(VDW )=-197.287 E(ELEC)=-137.022 | | E(CDIH)=1.197 E(NOE )=116.680 E(PLAN)=13.164 | ------------------------------------------------------------------------------- %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61973 intra-atom interactions %atoms "A -11 -ADE -O2' " and "A -12 -URI -H6 " only 1.33 A apart NBONDS: found 61965 intra-atom interactions --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =10.865 grad(E)=14.997 E(BOND)=34.053 E(ANGL)=157.999 | | E(DIHE)=0.000 E(IMPR)=20.550 E(VDW )=-195.654 E(ELEC)=-134.237 | | E(CDIH)=0.748 E(NOE )=115.112 E(PLAN)=12.295 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =-29.033 grad(E)=4.138 E(BOND)=16.612 E(ANGL)=139.192 | | E(DIHE)=0.000 E(IMPR)=17.167 E(VDW )=-195.587 E(ELEC)=-135.429 | | E(CDIH)=0.733 E(NOE )=116.007 E(PLAN)=12.272 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =-35.076 grad(E)=1.060 E(BOND)=15.668 E(ANGL)=137.655 | | E(DIHE)=0.000 E(IMPR)=17.208 E(VDW )=-198.762 E(ELEC)=-135.850 | | E(CDIH)=0.778 E(NOE )=116.194 E(PLAN)=12.033 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =-38.298 grad(E)=1.836 E(BOND)=15.697 E(ANGL)=136.859 | | E(DIHE)=0.000 E(IMPR)=16.897 E(VDW )=-200.898 E(ELEC)=-138.315 | | E(CDIH)=0.776 E(NOE )=119.171 E(PLAN)=11.514 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =-41.253 grad(E)=0.919 E(BOND)=15.771 E(ANGL)=136.172 | | E(DIHE)=0.000 E(IMPR)=16.591 E(VDW )=-202.722 E(ELEC)=-140.671 | | E(CDIH)=0.940 E(NOE )=121.612 E(PLAN)=11.054 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =-42.852 grad(E)=1.429 E(BOND)=15.607 E(ANGL)=136.799 | | E(DIHE)=0.000 E(IMPR)=16.993 E(VDW )=-204.524 E(ELEC)=-141.840 | | E(CDIH)=1.012 E(NOE )=121.925 E(PLAN)=11.176 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Analyze and write out the final structure. X-PLOR> X-PLOR>print threshold=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.050: 0 RMS deviation= 0.003 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.311809E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (A 10 C4' |A 10 C3' |A 10 O3' ) 118.992 110.500 8.492 9.777 445.032 (A 11 C4' |A 11 C3' |A 11 O3' ) 116.048 110.500 5.548 4.173 445.032 Number of violations greater 5.000: 2 RMS deviation= 0.824 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.823723 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 2.00000 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.448 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.448135 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 9 URI H1' set-j-atoms A 10 CYT H2' R= 5.333 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.333 E(NOE)= 11.079 ======================================== set-i-atoms A 10 CYT H3' set-j-atoms A 11 ADE H8 R= 3.394 NOE= 2.40 (- 0.60/+ 0.60) Delta= -0.394 E(NOE)= 15.535 ======================================== set-i-atoms A 11 ADE H2 set-j-atoms A 12 URI H1' R= 5.413 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.413 E(NOE)= 17.039 ======================================== set-i-atoms A 11 ADE H8 set-j-atoms A 12 URI H6 R= 5.477 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.477 E(NOE)= 22.766 ======================================== set-i-atoms A 12 URI H2' set-j-atoms A 13 ADE H8 R= 2.762 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.238 E(NOE)= 5.667 ======================================== set-i-atoms A 12 URI H3' set-j-atoms A 13 ADE H8 R= 3.346 NOE= 2.40 (- 0.60/+ 0.60) Delta= -0.346 E(NOE)= 11.982 ======================================== set-i-atoms A 13 ADE H8 set-j-atoms A 13 ADE H4' R= 4.203 NOE= 3.00 (- 1.00/+ 1.00) Delta= -0.203 E(NOE)= 4.128 ======================================== set-i-atoms A 11 ADE H1' set-j-atoms A 12 URI H6 R= 2.667 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.333 E(NOE)= 11.059 NOEPRI: RMS diff. = 0.036, #(violat.> 0.2)= 8 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.036, #(viol.> 0.2)= 8 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.362470E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 8.00000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 0 RMS deviation= 0.143 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.143057 (real) X-PLOR>evaluate ($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 15.6069, angle 136.799, dihedral 0, improper 16.993, NOE 121.925, c-dihedral 1.01242, planar 11.1758, VdW -204.524, elec -141.84, total -42.8518 RMSD: bond 3.118086E-03, angle 0.823723, dihedral 0, improper 0.448135, NOE 3.624701E-02, c-dihedral 0.143057 Violations: bond 0, angle 2, dihedral 0, improper 0, NOE 8, 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= 2822.3013 s X-PLOR: entry time at 08:02:39 17-Aug-96 X-PLOR: exit time at 08:50:25 17-Aug-96