X-PLOR: V3.840 user: on: Alpha/OSF at: 17-Aug-96 09:53:58 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=107087.094085693 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 20:17:48 created by user: COOR>ATOM 1 P GUA A 1 -5.655 9.296 3.972 1.00 0.00 A COOR>ATOM 2 O1P GUA A 1 -6.193 9.756 2.666 1.00 0.00 A X-PLOR> ! END in PDB file X-PLOR> X-PLOR>flags exclude * include bond angl dihe impr vdw elec noe cdih plan end X-PLOR> X-PLOR>! Intial minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved CODIMP: improper type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 2090 exclusions and 1650 interactions(1-4) %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65507 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =-154.355 grad(E)=3.898 E(BOND)=10.195 E(ANGL)=106.025 | | E(DIHE)=0.000 E(IMPR)=18.698 E(VDW )=-248.857 E(ELEC)=-102.267 | | E(CDIH)=2.346 E(NOE )=48.559 E(PLAN)=10.945 | ------------------------------------------------------------------------------- --------------- cycle= 50 ------ stepsize= 0.0001 ----------------------- | Etotal =-169.804 grad(E)=3.411 E(BOND)=8.795 E(ANGL)=102.702 | | E(DIHE)=0.000 E(IMPR)=16.143 E(VDW )=-258.099 E(ELEC)=-104.404 | | E(CDIH)=1.919 E(NOE )=50.279 E(PLAN)=12.863 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0000 ----------------------- | Etotal =-177.623 grad(E)=2.733 E(BOND)=7.623 E(ANGL)=100.025 | | E(DIHE)=0.000 E(IMPR)=16.854 E(VDW )=-260.050 E(ELEC)=-106.632 | | E(CDIH)=2.111 E(NOE )=49.063 E(PLAN)=13.383 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0001 ----------------------- | Etotal =-184.151 grad(E)=3.121 E(BOND)=7.710 E(ANGL)=100.068 | | E(DIHE)=0.000 E(IMPR)=17.870 E(VDW )=-262.673 E(ELEC)=-111.051 | | E(CDIH)=1.968 E(NOE )=48.230 E(PLAN)=13.728 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0000 ----------------------- | Etotal =-188.724 grad(E)=2.122 E(BOND)=7.565 E(ANGL)=99.189 | | E(DIHE)=0.000 E(IMPR)=18.402 E(VDW )=-262.054 E(ELEC)=-114.356 | | E(CDIH)=1.727 E(NOE )=47.097 E(PLAN)=13.707 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0001 ----------------------- | Etotal =-192.776 grad(E)=2.278 E(BOND)=7.925 E(ANGL)=99.721 | | E(DIHE)=0.000 E(IMPR)=17.455 E(VDW )=-261.415 E(ELEC)=-118.193 | | E(CDIH)=1.748 E(NOE )=46.357 E(PLAN)=13.626 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0000 ----------------------- | Etotal =-195.740 grad(E)=1.537 E(BOND)=7.824 E(ANGL)=99.307 | | E(DIHE)=0.000 E(IMPR)=17.247 E(VDW )=-260.139 E(ELEC)=-120.526 | | E(CDIH)=1.801 E(NOE )=45.614 E(PLAN)=13.132 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0001 ----------------------- | Etotal =-198.331 grad(E)=1.412 E(BOND)=8.330 E(ANGL)=100.573 | | E(DIHE)=0.000 E(IMPR)=17.176 E(VDW )=-262.217 E(ELEC)=-122.624 | | E(CDIH)=1.471 E(NOE )=45.948 E(PLAN)=13.012 | ------------------------------------------------------------------------------- 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= 0.108077094E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 0.06896 -0.01173 0.04912 velocity [A/ps] : 0.14177 -0.05835 -0.23883 ang. mom. [amu A/ps] : -1650.67850 -2394.80511 15218.60964 kin. ener. [Kcal/mol] : 0.64923 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 0.06896 -0.01173 0.04912 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)=377.188 E(kin)=575.520 temperature=285.194 | | Etotal =-198.331 grad(E)=1.412 E(BOND)=8.330 E(ANGL)=100.573 | | E(DIHE)=0.000 E(IMPR)=17.176 E(VDW )=-262.217 E(ELEC)=-122.624 | | E(CDIH)=1.471 E(NOE )=45.948 E(PLAN)=13.012 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65852 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65827 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65801 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65773 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65788 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65759 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65721 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65699 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65704 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65727 intra-atom interactions WRITEC: CORD sets starting from step 200 are written every 200 steps WRITEC: where 677 atoms are "free" %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 65737 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65772 intra-atom interactions --------------- step= 250 at 0.12500 ps -------------------------------- | E(kin)+E(total)=1026.654 E(kin)=594.831 temperature=294.764 | | Etotal =431.824 grad(E)=65.245 E(BOND)=200.416 E(ANGL)=382.108 | | E(DIHE)=0.000 E(IMPR)=96.199 E(VDW )=-244.877 E(ELEC)=-100.391 | | E(CDIH)=4.851 E(NOE )=81.979 E(PLAN)=11.539 | ------------------------------------------------------------------------------- NBONDS: found 65802 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65869 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65932 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66018 intra-atom interactions NBONDS: found 66148 intra-atom interactions NBONDS: found 66220 intra-atom interactions NBONDS: found 66230 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66228 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66149 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66113 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66018 intra-atom interactions --------------- step= 500 at 0.25000 ps -------------------------------- | E(kin)+E(total)=992.705 E(kin)=621.010 temperature=307.737 | | Etotal =371.694 grad(E)=64.786 E(BOND)=177.941 E(ANGL)=358.836 | | E(DIHE)=0.000 E(IMPR)=100.580 E(VDW )=-243.057 E(ELEC)=-125.966 | | E(CDIH)=11.142 E(NOE )=73.924 E(PLAN)=18.293 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65907 intra-atom interactions NBONDS: found 65826 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65795 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 65715 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.48 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65717 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.44 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.34 A apart NBONDS: found 65786 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.46 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.34 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65816 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart NBONDS: found 65788 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65912 intra-atom interactions --------------- step= 750 at 0.37500 ps -------------------------------- | E(kin)+E(total)=988.291 E(kin)=595.722 temperature=295.205 | | Etotal =392.569 grad(E)=63.892 E(BOND)=193.208 E(ANGL)=365.959 | | E(DIHE)=0.000 E(IMPR)=94.718 E(VDW )=-250.902 E(ELEC)=-129.485 | | E(CDIH)=1.376 E(NOE )=88.483 E(PLAN)=29.213 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 66034 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 66083 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66095 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66106 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 66193 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66247 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66293 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 66316 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66337 intra-atom interactions NBONDS: found 66355 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66310 intra-atom interactions --------------- step= 1000 at 0.50000 ps -------------------------------- | E(kin)+E(total)=977.107 E(kin)=575.665 temperature=285.266 | | Etotal =401.442 grad(E)=65.942 E(BOND)=204.353 E(ANGL)=377.492 | | E(DIHE)=0.000 E(IMPR)=95.081 E(VDW )=-255.904 E(ELEC)=-137.350 | | E(CDIH)=5.118 E(NOE )=93.085 E(PLAN)=19.567 | ------------------------------------------------------------------------------- NBONDS: found 66281 intra-atom interactions NBONDS: found 66194 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66123 intra-atom interactions NBONDS: found 66050 intra-atom interactions NBONDS: found 66000 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65897 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.50 A apart NBONDS: found 65804 intra-atom interactions NBONDS: found 65770 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart NBONDS: found 65704 intra-atom interactions NBONDS: found 65664 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65601 intra-atom interactions --------------- step= 1250 at 0.62500 ps -------------------------------- | E(kin)+E(total)=987.866 E(kin)=619.452 temperature=306.965 | | Etotal =368.414 grad(E)=62.534 E(BOND)=207.058 E(ANGL)=359.185 | | E(DIHE)=0.000 E(IMPR)=86.352 E(VDW )=-254.051 E(ELEC)=-126.656 | | E(CDIH)=1.401 E(NOE )=79.200 E(PLAN)=15.926 | ------------------------------------------------------------------------------- NBONDS: found 65634 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65641 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65576 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65666 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65667 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65676 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65619 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65598 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65630 intra-atom interactions --------------- step= 1500 at 0.75000 ps -------------------------------- | E(kin)+E(total)=996.410 E(kin)=604.980 temperature=299.793 | | Etotal =391.430 grad(E)=64.293 E(BOND)=221.961 E(ANGL)=345.918 | | E(DIHE)=0.000 E(IMPR)=99.691 E(VDW )=-254.339 E(ELEC)=-124.085 | | E(CDIH)=3.843 E(NOE )=83.631 E(PLAN)=14.810 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 65614 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart NBONDS: found 65622 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65582 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65645 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65665 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65620 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65668 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65614 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65556 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65479 intra-atom interactions --------------- step= 1750 at 0.87500 ps -------------------------------- | E(kin)+E(total)=993.464 E(kin)=621.944 temperature=308.199 | | Etotal =371.520 grad(E)=61.825 E(BOND)=208.520 E(ANGL)=347.051 | | E(DIHE)=0.000 E(IMPR)=88.855 E(VDW )=-237.343 E(ELEC)=-141.366 | | E(CDIH)=6.159 E(NOE )=79.999 E(PLAN)=19.647 | ------------------------------------------------------------------------------- NBONDS: found 65407 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65359 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65311 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65225 intra-atom interactions NBONDS: found 65199 intra-atom interactions NBONDS: found 65173 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65158 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65174 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65223 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65332 intra-atom interactions --------------- step= 2000 at 1.00000 ps -------------------------------- | E(kin)+E(total)=995.111 E(kin)=618.252 temperature=306.370 | | Etotal =376.859 grad(E)=64.194 E(BOND)=202.812 E(ANGL)=343.848 | | E(DIHE)=0.000 E(IMPR)=100.830 E(VDW )=-232.347 E(ELEC)=-127.540 | | E(CDIH)=5.110 E(NOE )=64.876 E(PLAN)=19.272 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65456 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65561 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65648 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65694 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65691 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65654 intra-atom interactions NBONDS: found 65591 intra-atom interactions --------------- step= 2250 at 1.12500 ps -------------------------------- | E(kin)+E(total)=1009.771 E(kin)=600.029 temperature=297.339 | | Etotal =409.742 grad(E)=65.808 E(BOND)=205.451 E(ANGL)=370.784 | | E(DIHE)=0.000 E(IMPR)=91.903 E(VDW )=-246.788 E(ELEC)=-124.000 | | E(CDIH)=3.356 E(NOE )=90.683 E(PLAN)=18.352 | ------------------------------------------------------------------------------- NBONDS: found 65640 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65613 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 65483 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.39 A apart NBONDS: found 65495 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.42 A apart NBONDS: found 65523 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65518 intra-atom interactions NBONDS: found 65460 intra-atom interactions --------------- step= 2500 at 1.25000 ps -------------------------------- | E(kin)+E(total)=996.428 E(kin)=615.647 temperature=305.079 | | Etotal =380.781 grad(E)=63.536 E(BOND)=187.103 E(ANGL)=387.773 | | E(DIHE)=0.000 E(IMPR)=90.629 E(VDW )=-246.458 E(ELEC)=-129.972 | | E(CDIH)=4.632 E(NOE )=64.361 E(PLAN)=22.711 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=987.027 E(kin)=603.159 temperature=298.891 | | Etotal =383.867 grad(E)=64.047 E(BOND)=199.297 E(ANGL)=359.545 | | E(DIHE)=0.000 E(IMPR)=93.689 E(VDW )=-245.064 E(ELEC)=-125.899 | | E(CDIH)=3.926 E(NOE )=79.316 E(PLAN)=19.056 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=44.002 E(kin)=22.322 temperature=11.062 | | Etotal =31.359 grad(E)=1.958 E(BOND)=13.329 E(ANGL)=16.476 | | E(DIHE)=0.000 E(IMPR)=7.046 E(VDW )=7.963 E(ELEC)=8.882 | | E(CDIH)=1.991 E(NOE )=7.924 E(PLAN)=3.419 | ------------------------------------------------------------------------------- NBONDS: found 65499 intra-atom interactions NBONDS: found 65499 intra-atom interactions NBONDS: found 65513 intra-atom interactions NBONDS: found 65621 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65599 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65675 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65808 intra-atom interactions --------------- step= 2750 at 1.37500 ps -------------------------------- | E(kin)+E(total)=969.560 E(kin)=608.725 temperature=301.649 | | Etotal =360.835 grad(E)=62.574 E(BOND)=191.276 E(ANGL)=370.658 | | E(DIHE)=0.000 E(IMPR)=81.892 E(VDW )=-247.130 E(ELEC)=-137.501 | | E(CDIH)=6.163 E(NOE )=78.164 E(PLAN)=17.313 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65905 intra-atom interactions NBONDS: found 66034 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66012 intra-atom interactions NBONDS: found 65990 intra-atom interactions NBONDS: found 65880 intra-atom interactions NBONDS: found 65851 intra-atom interactions --------------- step= 3000 at 1.50000 ps -------------------------------- | E(kin)+E(total)=993.668 E(kin)=612.417 temperature=303.478 | | Etotal =381.251 grad(E)=63.807 E(BOND)=201.835 E(ANGL)=356.584 | | E(DIHE)=0.000 E(IMPR)=88.057 E(VDW )=-243.216 E(ELEC)=-125.056 | | E(CDIH)=2.871 E(NOE )=79.343 E(PLAN)=20.832 | ------------------------------------------------------------------------------- NBONDS: found 65874 intra-atom interactions NBONDS: found 65802 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart NBONDS: found 65839 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65842 intra-atom interactions NBONDS: found 65747 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65749 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65753 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65800 intra-atom interactions NBONDS: found 65886 intra-atom interactions --------------- step= 3250 at 1.62500 ps -------------------------------- | E(kin)+E(total)=994.648 E(kin)=580.557 temperature=287.690 | | Etotal =414.090 grad(E)=66.283 E(BOND)=225.205 E(ANGL)=369.182 | | E(DIHE)=0.000 E(IMPR)=89.551 E(VDW )=-248.239 E(ELEC)=-122.793 | | E(CDIH)=3.562 E(NOE )=76.426 E(PLAN)=21.196 | ------------------------------------------------------------------------------- NBONDS: found 65920 intra-atom interactions NBONDS: found 65973 intra-atom interactions NBONDS: found 65929 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65918 intra-atom interactions NBONDS: found 65899 intra-atom interactions NBONDS: found 65819 intra-atom interactions NBONDS: found 65823 intra-atom interactions --------------- step= 3500 at 1.75000 ps -------------------------------- | E(kin)+E(total)=1002.378 E(kin)=613.360 temperature=303.946 | | Etotal =389.018 grad(E)=64.518 E(BOND)=202.431 E(ANGL)=363.355 | | E(DIHE)=0.000 E(IMPR)=96.014 E(VDW )=-260.582 E(ELEC)=-111.374 | | E(CDIH)=1.809 E(NOE )=76.567 E(PLAN)=20.798 | ------------------------------------------------------------------------------- NBONDS: found 65828 intra-atom interactions NBONDS: found 65792 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65726 intra-atom interactions NBONDS: found 65661 intra-atom interactions NBONDS: found 65700 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65672 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65686 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65713 intra-atom interactions --------------- step= 3750 at 1.87500 ps -------------------------------- | E(kin)+E(total)=988.141 E(kin)=578.656 temperature=286.748 | | Etotal =409.485 grad(E)=67.960 E(BOND)=211.836 E(ANGL)=381.937 | | E(DIHE)=0.000 E(IMPR)=101.567 E(VDW )=-256.197 E(ELEC)=-117.513 | | E(CDIH)=3.632 E(NOE )=68.907 E(PLAN)=15.315 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65805 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65778 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65771 intra-atom interactions NBONDS: found 65755 intra-atom interactions NBONDS: found 65783 intra-atom interactions NBONDS: found 65846 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65793 intra-atom interactions NBONDS: found 65871 intra-atom interactions --------------- step= 4000 at 2.00000 ps -------------------------------- | E(kin)+E(total)=1011.723 E(kin)=594.930 temperature=294.813 | | Etotal =416.794 grad(E)=65.337 E(BOND)=223.898 E(ANGL)=376.582 | | E(DIHE)=0.000 E(IMPR)=94.118 E(VDW )=-263.052 E(ELEC)=-122.289 | | E(CDIH)=2.157 E(NOE )=86.651 E(PLAN)=18.730 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65911 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65972 intra-atom interactions NBONDS: found 65981 intra-atom interactions NBONDS: found 66030 intra-atom interactions NBONDS: found 66072 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66244 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66361 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 66460 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 66523 intra-atom interactions --------------- step= 4250 at 2.12500 ps -------------------------------- | E(kin)+E(total)=1009.442 E(kin)=602.032 temperature=298.332 | | Etotal =407.410 grad(E)=65.257 E(BOND)=206.420 E(ANGL)=380.977 | | E(DIHE)=0.000 E(IMPR)=91.772 E(VDW )=-246.406 E(ELEC)=-124.647 | | E(CDIH)=5.844 E(NOE )=76.849 E(PLAN)=16.601 | ------------------------------------------------------------------------------- NBONDS: found 66632 intra-atom interactions NBONDS: found 66681 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart NBONDS: found 66682 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66667 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 66707 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66711 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66692 intra-atom interactions NBONDS: found 66687 intra-atom interactions --------------- step= 4500 at 2.25000 ps -------------------------------- | E(kin)+E(total)=1000.985 E(kin)=619.339 temperature=306.909 | | Etotal =381.646 grad(E)=64.801 E(BOND)=219.894 E(ANGL)=342.515 | | E(DIHE)=0.000 E(IMPR)=87.843 E(VDW )=-250.601 E(ELEC)=-121.399 | | E(CDIH)=3.735 E(NOE )=83.282 E(PLAN)=16.377 | ------------------------------------------------------------------------------- NBONDS: found 66642 intra-atom interactions NBONDS: found 66593 intra-atom interactions NBONDS: found 66521 intra-atom interactions NBONDS: found 66465 intra-atom interactions NBONDS: found 66516 intra-atom interactions NBONDS: found 66511 intra-atom interactions NBONDS: found 66571 intra-atom interactions NBONDS: found 66656 intra-atom interactions --------------- step= 4750 at 2.37500 ps -------------------------------- | E(kin)+E(total)=984.372 E(kin)=613.470 temperature=304.000 | | Etotal =370.903 grad(E)=64.583 E(BOND)=201.238 E(ANGL)=354.522 | | E(DIHE)=0.000 E(IMPR)=101.282 E(VDW )=-261.379 E(ELEC)=-124.591 | | E(CDIH)=3.590 E(NOE )=79.573 E(PLAN)=16.668 | ------------------------------------------------------------------------------- NBONDS: found 66809 intra-atom interactions NBONDS: found 66820 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66819 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66795 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66829 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.35 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66781 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66821 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66769 intra-atom interactions --------------- step= 5000 at 2.50000 ps -------------------------------- | E(kin)+E(total)=993.177 E(kin)=582.692 temperature=288.749 | | Etotal =410.484 grad(E)=68.102 E(BOND)=217.610 E(ANGL)=375.890 | | E(DIHE)=0.000 E(IMPR)=98.439 E(VDW )=-243.768 E(ELEC)=-127.309 | | E(CDIH)=6.088 E(NOE )=63.566 E(PLAN)=19.967 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=996.045 E(kin)=605.476 temperature=300.039 | | Etotal =390.569 grad(E)=64.872 E(BOND)=206.349 E(ANGL)=366.586 | | E(DIHE)=0.000 E(IMPR)=93.847 E(VDW )=-252.057 E(ELEC)=-122.448 | | E(CDIH)=3.669 E(NOE )=76.535 E(PLAN)=18.088 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=13.748 E(kin)=12.676 temperature=6.282 | | Etotal =18.242 grad(E)=1.397 E(BOND)=9.673 E(ANGL)=12.784 | | E(DIHE)=0.000 E(IMPR)=6.585 E(VDW )=6.789 E(ELEC)=6.342 | | E(CDIH)=1.834 E(NOE )=7.094 E(PLAN)=2.575 | ------------------------------------------------------------------------------- --------------- averages for last 5000 steps ----------------------------- | E(kin)+E(total)=991.536 E(kin)=604.318 temperature=299.465 | | Etotal =387.218 grad(E)=64.460 E(BOND)=202.823 E(ANGL)=363.066 | | E(DIHE)=0.000 E(IMPR)=93.768 E(VDW )=-248.561 E(ELEC)=-124.173 | | E(CDIH)=3.798 E(NOE )=77.925 E(PLAN)=18.572 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5000 steps ----------------------- | E(kin)+E(total)=32.908 E(kin)=18.189 temperature=9.013 | | Etotal =25.871 grad(E)=1.750 E(BOND)=12.168 E(ANGL)=15.160 | | E(DIHE)=0.000 E(IMPR)=6.820 E(VDW )=8.184 E(ELEC)=7.908 | | E(CDIH)=1.919 E(NOE )=7.648 E(PLAN)=3.065 | ------------------------------------------------------------------------------- NBONDS: found 66806 intra-atom interactions NBONDS: found 66842 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart NBONDS: found 66883 intra-atom interactions NBONDS: found 66821 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 66797 intra-atom interactions NBONDS: found 66818 intra-atom interactions NBONDS: found 66800 intra-atom interactions NBONDS: found 66787 intra-atom interactions --------------- step= 5250 at 2.62500 ps -------------------------------- | E(kin)+E(total)=1013.096 E(kin)=625.350 temperature=309.887 | | Etotal =387.746 grad(E)=64.453 E(BOND)=210.791 E(ANGL)=366.662 | | E(DIHE)=0.000 E(IMPR)=90.716 E(VDW )=-244.049 E(ELEC)=-133.604 | | E(CDIH)=5.351 E(NOE )=71.574 E(PLAN)=20.305 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66698 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66653 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66544 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66446 intra-atom interactions NBONDS: found 66375 intra-atom interactions NBONDS: found 66258 intra-atom interactions NBONDS: found 66244 intra-atom interactions NBONDS: found 66228 intra-atom interactions --------------- step= 5500 at 2.75000 ps -------------------------------- | E(kin)+E(total)=995.518 E(kin)=594.664 temperature=294.681 | | Etotal =400.854 grad(E)=66.517 E(BOND)=210.110 E(ANGL)=387.636 | | E(DIHE)=0.000 E(IMPR)=93.561 E(VDW )=-268.109 E(ELEC)=-119.396 | | E(CDIH)=4.593 E(NOE )=72.419 E(PLAN)=20.040 | ------------------------------------------------------------------------------- NBONDS: found 66261 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66306 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66344 intra-atom interactions NBONDS: found 66406 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66386 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66314 intra-atom interactions NBONDS: found 66301 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66258 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66210 intra-atom interactions --------------- step= 5750 at 2.87500 ps -------------------------------- | E(kin)+E(total)=992.294 E(kin)=632.419 temperature=313.390 | | Etotal =359.875 grad(E)=64.747 E(BOND)=214.436 E(ANGL)=344.906 | | E(DIHE)=0.000 E(IMPR)=83.077 E(VDW )=-258.992 E(ELEC)=-121.003 | | E(CDIH)=2.214 E(NOE )=73.888 E(PLAN)=21.348 | ------------------------------------------------------------------------------- NBONDS: found 66147 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart NBONDS: found 66097 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart NBONDS: found 66044 intra-atom interactions NBONDS: found 65991 intra-atom interactions NBONDS: found 65940 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65917 intra-atom interactions NBONDS: found 65877 intra-atom interactions NBONDS: found 65898 intra-atom interactions NBONDS: found 65903 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65896 intra-atom interactions NBONDS: found 65906 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart NBONDS: found 65952 intra-atom interactions --------------- step= 6000 at 3.00000 ps -------------------------------- | E(kin)+E(total)=976.134 E(kin)=617.968 temperature=306.229 | | Etotal =358.166 grad(E)=65.050 E(BOND)=190.679 E(ANGL)=364.807 | | E(DIHE)=0.000 E(IMPR)=91.029 E(VDW )=-253.590 E(ELEC)=-127.635 | | E(CDIH)=4.292 E(NOE )=72.070 E(PLAN)=16.515 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.43 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65983 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 66034 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66095 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 66117 intra-atom interactions NBONDS: found 66102 intra-atom interactions NBONDS: found 66176 intra-atom interactions NBONDS: found 66166 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66210 intra-atom interactions --------------- step= 6250 at 3.12500 ps -------------------------------- | E(kin)+E(total)=990.172 E(kin)=595.878 temperature=295.282 | | Etotal =394.294 grad(E)=67.079 E(BOND)=216.206 E(ANGL)=368.642 | | E(DIHE)=0.000 E(IMPR)=90.057 E(VDW )=-254.049 E(ELEC)=-138.805 | | E(CDIH)=2.746 E(NOE )=89.957 E(PLAN)=19.542 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66293 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66281 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 66287 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart NBONDS: found 66294 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.35 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 66196 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 66147 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66078 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65978 intra-atom interactions --------------- step= 6500 at 3.25000 ps -------------------------------- | E(kin)+E(total)=990.001 E(kin)=595.361 temperature=295.026 | | Etotal =394.640 grad(E)=69.021 E(BOND)=224.983 E(ANGL)=362.776 | | E(DIHE)=0.000 E(IMPR)=79.115 E(VDW )=-239.009 E(ELEC)=-134.549 | | E(CDIH)=3.961 E(NOE )=70.859 E(PLAN)=26.504 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65863 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65772 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65726 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65723 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65696 intra-atom interactions NBONDS: found 65611 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65609 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65544 intra-atom interactions --------------- step= 6750 at 3.37500 ps -------------------------------- | E(kin)+E(total)=994.493 E(kin)=611.369 temperature=302.959 | | Etotal =383.125 grad(E)=66.474 E(BOND)=215.521 E(ANGL)=351.639 | | E(DIHE)=0.000 E(IMPR)=94.662 E(VDW )=-267.457 E(ELEC)=-124.703 | | E(CDIH)=4.114 E(NOE )=88.641 E(PLAN)=20.708 | ------------------------------------------------------------------------------- NBONDS: found 65558 intra-atom interactions NBONDS: found 65586 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65616 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65720 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65745 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65820 intra-atom interactions --------------- step= 7000 at 3.50000 ps -------------------------------- | E(kin)+E(total)=984.818 E(kin)=605.517 temperature=300.059 | | Etotal =379.301 grad(E)=67.450 E(BOND)=207.934 E(ANGL)=363.521 | | E(DIHE)=0.000 E(IMPR)=91.509 E(VDW )=-244.100 E(ELEC)=-132.356 | | E(CDIH)=5.678 E(NOE )=64.725 E(PLAN)=22.390 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65775 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65689 intra-atom interactions NBONDS: found 65677 intra-atom interactions NBONDS: found 65699 intra-atom interactions NBONDS: found 65702 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65713 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65735 intra-atom interactions --------------- step= 7250 at 3.62500 ps -------------------------------- | E(kin)+E(total)=991.863 E(kin)=613.363 temperature=303.947 | | Etotal =378.500 grad(E)=67.452 E(BOND)=226.166 E(ANGL)=354.515 | | E(DIHE)=0.000 E(IMPR)=93.820 E(VDW )=-254.594 E(ELEC)=-134.893 | | E(CDIH)=1.950 E(NOE )=67.580 E(PLAN)=23.955 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65750 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65785 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.38 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65847 intra-atom interactions NBONDS: found 65917 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66004 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart NBONDS: found 65905 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.44 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65850 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65738 intra-atom interactions --------------- step= 7500 at 3.75000 ps -------------------------------- | E(kin)+E(total)=998.589 E(kin)=601.800 temperature=298.217 | | Etotal =396.789 grad(E)=66.679 E(BOND)=204.451 E(ANGL)=385.691 | | E(DIHE)=0.000 E(IMPR)=90.096 E(VDW )=-245.279 E(ELEC)=-133.780 | | E(CDIH)=4.948 E(NOE )=69.875 E(PLAN)=20.787 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=995.570 E(kin)=605.459 temperature=300.030 | | Etotal =390.111 grad(E)=66.510 E(BOND)=213.032 E(ANGL)=368.609 | | E(DIHE)=0.000 E(IMPR)=91.947 E(VDW )=-252.787 E(ELEC)=-130.115 | | E(CDIH)=3.689 E(NOE )=75.219 E(PLAN)=20.519 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.523 E(kin)=11.894 temperature=5.894 | | Etotal =14.254 grad(E)=1.431 E(BOND)=9.434 E(ANGL)=11.612 | | E(DIHE)=0.000 E(IMPR)=6.457 E(VDW )=7.182 E(ELEC)=4.986 | | E(CDIH)=1.956 E(NOE )=7.974 E(PLAN)=2.776 | ------------------------------------------------------------------------------- --------------- averages for last 7500 steps ----------------------------- | E(kin)+E(total)=992.881 E(kin)=604.698 temperature=299.653 | | Etotal =388.183 grad(E)=65.143 E(BOND)=206.226 E(ANGL)=364.914 | | E(DIHE)=0.000 E(IMPR)=93.161 E(VDW )=-249.970 E(ELEC)=-126.154 | | E(CDIH)=3.761 E(NOE )=77.023 E(PLAN)=19.221 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 7500 steps ----------------------- | E(kin)+E(total)=27.382 E(kin)=16.371 temperature=8.112 | | Etotal =22.711 grad(E)=1.913 E(BOND)=12.310 E(ANGL)=14.318 | | E(DIHE)=0.000 E(IMPR)=6.756 E(VDW )=8.112 E(ELEC)=7.604 | | E(CDIH)=1.932 E(NOE )=7.862 E(PLAN)=3.110 | ------------------------------------------------------------------------------- %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65713 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65670 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65595 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65582 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65566 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65661 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65793 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65876 intra-atom interactions --------------- step= 7750 at 3.87500 ps -------------------------------- | E(kin)+E(total)=1016.899 E(kin)=618.543 temperature=306.514 | | Etotal =398.356 grad(E)=67.826 E(BOND)=218.746 E(ANGL)=374.511 | | E(DIHE)=0.000 E(IMPR)=87.626 E(VDW )=-246.582 E(ELEC)=-129.033 | | E(CDIH)=3.074 E(NOE )=70.810 E(PLAN)=19.203 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65946 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66016 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66068 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66193 intra-atom interactions NBONDS: found 66170 intra-atom interactions NBONDS: found 66168 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66208 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 66167 intra-atom interactions --------------- step= 8000 at 4.00000 ps -------------------------------- | E(kin)+E(total)=1003.602 E(kin)=611.223 temperature=302.887 | | Etotal =392.380 grad(E)=69.120 E(BOND)=207.410 E(ANGL)=383.848 | | E(DIHE)=0.000 E(IMPR)=97.856 E(VDW )=-269.051 E(ELEC)=-129.040 | | E(CDIH)=3.166 E(NOE )=78.457 E(PLAN)=19.735 | ------------------------------------------------------------------------------- NBONDS: found 66172 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66133 intra-atom interactions NBONDS: found 66173 intra-atom interactions NBONDS: found 66221 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66187 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.45 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 66171 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.32 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66266 intra-atom interactions --------------- step= 8250 at 4.12500 ps -------------------------------- | E(kin)+E(total)=984.413 E(kin)=601.666 temperature=298.151 | | Etotal =382.748 grad(E)=67.320 E(BOND)=217.915 E(ANGL)=349.181 | | E(DIHE)=0.000 E(IMPR)=95.481 E(VDW )=-248.998 E(ELEC)=-127.803 | | E(CDIH)=3.218 E(NOE )=75.766 E(PLAN)=17.986 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart NBONDS: found 66295 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.35 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66345 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.37 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart NBONDS: found 66451 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66519 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66542 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 66557 intra-atom interactions NBONDS: found 66626 intra-atom interactions NBONDS: found 66593 intra-atom interactions --------------- step= 8500 at 4.25000 ps -------------------------------- | E(kin)+E(total)=998.851 E(kin)=591.553 temperature=293.139 | | Etotal =407.298 grad(E)=68.140 E(BOND)=212.019 E(ANGL)=381.516 | | E(DIHE)=0.000 E(IMPR)=108.493 E(VDW )=-251.118 E(ELEC)=-131.288 | | E(CDIH)=3.033 E(NOE )=64.446 E(PLAN)=20.198 | ------------------------------------------------------------------------------- %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 66551 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66604 intra-atom interactions NBONDS: found 66622 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66604 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66609 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66585 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66536 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66491 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66529 intra-atom interactions --------------- step= 8750 at 4.37500 ps -------------------------------- | E(kin)+E(total)=1005.911 E(kin)=611.875 temperature=303.210 | | Etotal =394.036 grad(E)=64.649 E(BOND)=209.362 E(ANGL)=354.499 | | E(DIHE)=0.000 E(IMPR)=91.334 E(VDW )=-236.407 E(ELEC)=-127.657 | | E(CDIH)=6.369 E(NOE )=79.758 E(PLAN)=16.777 | ------------------------------------------------------------------------------- NBONDS: found 66434 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66470 intra-atom interactions NBONDS: found 66424 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66490 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66446 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 66406 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 66429 intra-atom interactions --------------- step= 9000 at 4.50000 ps -------------------------------- | E(kin)+E(total)=999.251 E(kin)=602.798 temperature=298.712 | | Etotal =396.453 grad(E)=65.971 E(BOND)=214.529 E(ANGL)=373.932 | | E(DIHE)=0.000 E(IMPR)=93.225 E(VDW )=-246.993 E(ELEC)=-130.893 | | E(CDIH)=1.511 E(NOE )=76.335 E(PLAN)=14.808 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66475 intra-atom interactions NBONDS: found 66482 intra-atom interactions NBONDS: found 66527 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.39 A apart NBONDS: found 66531 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.37 A apart NBONDS: found 66522 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 66498 intra-atom interactions NBONDS: found 66376 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66371 intra-atom interactions --------------- step= 9250 at 4.62500 ps -------------------------------- | E(kin)+E(total)=985.556 E(kin)=604.002 temperature=299.308 | | Etotal =381.554 grad(E)=66.454 E(BOND)=208.998 E(ANGL)=371.786 | | E(DIHE)=0.000 E(IMPR)=90.732 E(VDW )=-254.269 E(ELEC)=-129.965 | | E(CDIH)=1.786 E(NOE )=74.676 E(PLAN)=17.811 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66283 intra-atom interactions NBONDS: found 66187 intra-atom interactions NBONDS: found 66124 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66107 intra-atom interactions NBONDS: found 66131 intra-atom interactions NBONDS: found 66136 intra-atom interactions NBONDS: found 66147 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66127 intra-atom interactions --------------- step= 9500 at 4.75000 ps -------------------------------- | E(kin)+E(total)=1007.402 E(kin)=608.816 temperature=301.694 | | Etotal =398.586 grad(E)=66.015 E(BOND)=199.972 E(ANGL)=397.479 | | E(DIHE)=0.000 E(IMPR)=73.777 E(VDW )=-244.001 E(ELEC)=-127.441 | | E(CDIH)=0.915 E(NOE )=73.766 E(PLAN)=24.121 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 66231 intra-atom interactions NBONDS: found 66179 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.44 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66183 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 66183 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 66215 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66203 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66176 intra-atom interactions --------------- step= 9750 at 4.87500 ps -------------------------------- | E(kin)+E(total)=1005.446 E(kin)=627.897 temperature=311.149 | | Etotal =377.550 grad(E)=65.322 E(BOND)=200.519 E(ANGL)=356.808 | | E(DIHE)=0.000 E(IMPR)=91.113 E(VDW )=-239.977 E(ELEC)=-126.882 | | E(CDIH)=2.765 E(NOE )=72.548 E(PLAN)=20.655 | ------------------------------------------------------------------------------- NBONDS: found 66155 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66155 intra-atom interactions NBONDS: found 66038 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65995 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart NBONDS: found 65930 intra-atom interactions --------------- step= 10000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=1020.957 E(kin)=636.850 temperature=315.586 | | Etotal =384.107 grad(E)=64.661 E(BOND)=219.486 E(ANGL)=381.892 | | E(DIHE)=0.000 E(IMPR)=76.896 E(VDW )=-265.161 E(ELEC)=-130.092 | | E(CDIH)=1.098 E(NOE )=79.224 E(PLAN)=20.763 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=998.279 E(kin)=605.397 temperature=300.000 | | Etotal =392.882 grad(E)=67.034 E(BOND)=212.980 E(ANGL)=369.270 | | E(DIHE)=0.000 E(IMPR)=94.408 E(VDW )=-249.908 E(ELEC)=-128.310 | | E(CDIH)=3.677 E(NOE )=72.184 E(PLAN)=18.580 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.661 E(kin)=11.974 temperature=5.933 | | Etotal =14.402 grad(E)=1.325 E(BOND)=9.069 E(ANGL)=13.120 | | E(DIHE)=0.000 E(IMPR)=6.518 E(VDW )=7.907 E(ELEC)=3.957 | | E(CDIH)=1.913 E(NOE )=7.729 E(PLAN)=2.175 | ------------------------------------------------------------------------------- --------------- averages for last 10000 steps ----------------------------- | E(kin)+E(total)=994.230 E(kin)=604.873 temperature=299.740 | | Etotal =389.358 grad(E)=65.616 E(BOND)=207.915 E(ANGL)=366.003 | | E(DIHE)=0.000 E(IMPR)=93.473 E(VDW )=-249.954 E(ELEC)=-126.693 | | E(CDIH)=3.740 E(NOE )=75.813 E(PLAN)=19.061 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10000 steps ----------------------- | E(kin)+E(total)=24.219 E(kin)=15.393 temperature=7.628 | | Etotal =21.044 grad(E)=1.963 E(BOND)=11.948 E(ANGL)=14.154 | | E(DIHE)=0.000 E(IMPR)=6.719 E(VDW )=8.062 E(ELEC)=6.939 | | E(CDIH)=1.928 E(NOE )=8.105 E(PLAN)=2.918 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66005 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66070 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 66101 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 66218 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66296 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 66369 intra-atom interactions --------------- step= 10250 at 5.12500 ps -------------------------------- | E(kin)+E(total)=997.623 E(kin)=601.023 temperature=297.832 | | Etotal =396.600 grad(E)=65.941 E(BOND)=199.912 E(ANGL)=382.820 | | E(DIHE)=0.000 E(IMPR)=94.425 E(VDW )=-237.149 E(ELEC)=-132.738 | | E(CDIH)=1.907 E(NOE )=69.231 E(PLAN)=18.192 | ------------------------------------------------------------------------------- %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 66444 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66392 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66438 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66399 intra-atom interactions NBONDS: found 66433 intra-atom interactions NBONDS: found 66453 intra-atom interactions --------------- step= 10500 at 5.25000 ps -------------------------------- | E(kin)+E(total)=993.099 E(kin)=611.677 temperature=303.112 | | Etotal =381.422 grad(E)=65.886 E(BOND)=206.192 E(ANGL)=375.476 | | E(DIHE)=0.000 E(IMPR)=95.175 E(VDW )=-244.593 E(ELEC)=-136.955 | | E(CDIH)=2.239 E(NOE )=63.750 E(PLAN)=20.137 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart NBONDS: found 66385 intra-atom interactions NBONDS: found 66234 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66175 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66068 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66079 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66036 intra-atom interactions --------------- step= 10750 at 5.37500 ps -------------------------------- | E(kin)+E(total)=992.021 E(kin)=605.273 temperature=299.938 | | Etotal =386.748 grad(E)=68.472 E(BOND)=208.203 E(ANGL)=364.018 | | E(DIHE)=0.000 E(IMPR)=99.865 E(VDW )=-242.021 E(ELEC)=-137.743 | | E(CDIH)=3.000 E(NOE )=70.749 E(PLAN)=20.677 | ------------------------------------------------------------------------------- NBONDS: found 65985 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65930 intra-atom interactions NBONDS: found 65889 intra-atom interactions NBONDS: found 65798 intra-atom interactions NBONDS: found 65712 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65600 intra-atom interactions --------------- step= 11000 at 5.50000 ps -------------------------------- | E(kin)+E(total)=1003.253 E(kin)=590.969 temperature=292.850 | | Etotal =412.284 grad(E)=67.951 E(BOND)=217.063 E(ANGL)=393.454 | | E(DIHE)=0.000 E(IMPR)=100.450 E(VDW )=-259.664 E(ELEC)=-129.540 | | E(CDIH)=3.515 E(NOE )=66.500 E(PLAN)=20.507 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65481 intra-atom interactions NBONDS: found 65356 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65280 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65222 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65134 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65119 intra-atom interactions --------------- step= 11250 at 5.62500 ps -------------------------------- | E(kin)+E(total)=1018.824 E(kin)=602.547 temperature=298.588 | | Etotal =416.277 grad(E)=67.795 E(BOND)=231.634 E(ANGL)=373.633 | | E(DIHE)=0.000 E(IMPR)=98.904 E(VDW )=-265.496 E(ELEC)=-120.321 | | E(CDIH)=4.204 E(NOE )=74.858 E(PLAN)=18.861 | ------------------------------------------------------------------------------- NBONDS: found 65262 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65273 intra-atom interactions NBONDS: found 65405 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65543 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65636 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65674 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.39 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65606 intra-atom interactions --------------- step= 11500 at 5.75000 ps -------------------------------- | E(kin)+E(total)=990.210 E(kin)=629.789 temperature=312.087 | | Etotal =360.420 grad(E)=66.298 E(BOND)=201.325 E(ANGL)=370.421 | | E(DIHE)=0.000 E(IMPR)=92.654 E(VDW )=-254.702 E(ELEC)=-135.101 | | E(CDIH)=3.192 E(NOE )=67.265 E(PLAN)=15.367 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65485 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65520 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65486 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65545 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 65589 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65741 intra-atom interactions --------------- step= 11750 at 5.87500 ps -------------------------------- | E(kin)+E(total)=985.513 E(kin)=599.543 temperature=297.099 | | Etotal =385.970 grad(E)=66.483 E(BOND)=189.815 E(ANGL)=379.904 | | E(DIHE)=0.000 E(IMPR)=108.475 E(VDW )=-248.782 E(ELEC)=-130.508 | | E(CDIH)=3.498 E(NOE )=61.149 E(PLAN)=22.418 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65832 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65926 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65971 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65977 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65975 intra-atom interactions --------------- step= 12000 at 6.00000 ps -------------------------------- | E(kin)+E(total)=995.322 E(kin)=611.129 temperature=302.840 | | Etotal =384.193 grad(E)=65.798 E(BOND)=224.263 E(ANGL)=354.304 | | E(DIHE)=0.000 E(IMPR)=88.071 E(VDW )=-245.435 E(ELEC)=-128.099 | | E(CDIH)=4.559 E(NOE )=67.917 E(PLAN)=18.613 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66004 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65963 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65866 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65742 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65796 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65738 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65761 intra-atom interactions --------------- step= 12250 at 6.12500 ps -------------------------------- | E(kin)+E(total)=995.841 E(kin)=600.171 temperature=297.410 | | Etotal =395.671 grad(E)=66.359 E(BOND)=214.740 E(ANGL)=382.952 | | E(DIHE)=0.000 E(IMPR)=91.950 E(VDW )=-247.599 E(ELEC)=-137.365 | | E(CDIH)=2.855 E(NOE )=67.227 E(PLAN)=20.911 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.44 A apart NBONDS: found 65793 intra-atom interactions NBONDS: found 65775 intra-atom interactions NBONDS: found 65689 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 65690 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.32 A apart NBONDS: found 65545 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65591 intra-atom interactions --------------- step= 12500 at 6.25000 ps -------------------------------- | E(kin)+E(total)=996.934 E(kin)=584.662 temperature=289.725 | | Etotal =412.272 grad(E)=66.260 E(BOND)=224.886 E(ANGL)=376.384 | | E(DIHE)=0.000 E(IMPR)=94.070 E(VDW )=-249.864 E(ELEC)=-137.109 | | E(CDIH)=3.735 E(NOE )=82.913 E(PLAN)=17.257 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=996.925 E(kin)=605.559 temperature=300.080 | | Etotal =391.366 grad(E)=66.228 E(BOND)=211.005 E(ANGL)=373.120 | | E(DIHE)=0.000 E(IMPR)=95.190 E(VDW )=-249.759 E(ELEC)=-132.141 | | E(CDIH)=3.898 E(NOE )=70.973 E(PLAN)=19.081 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.132 E(kin)=12.322 temperature=6.106 | | Etotal =14.833 grad(E)=1.301 E(BOND)=9.617 E(ANGL)=11.418 | | E(DIHE)=0.000 E(IMPR)=6.759 E(VDW )=7.052 E(ELEC)=5.705 | | E(CDIH)=2.019 E(NOE )=6.640 E(PLAN)=2.141 | ------------------------------------------------------------------------------- --------------- averages for last 12500 steps ----------------------------- | E(kin)+E(total)=994.769 E(kin)=605.010 temperature=299.808 | | Etotal =389.759 grad(E)=65.739 E(BOND)=208.533 E(ANGL)=367.426 | | E(DIHE)=0.000 E(IMPR)=93.816 E(VDW )=-249.915 E(ELEC)=-127.783 | | E(CDIH)=3.772 E(NOE )=74.845 E(PLAN)=19.065 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 12500 steps ----------------------- | E(kin)+E(total)=22.070 E(kin)=14.832 temperature=7.350 | | Etotal =19.973 grad(E)=1.866 E(BOND)=11.586 E(ANGL)=13.945 | | E(DIHE)=0.000 E(IMPR)=6.762 E(VDW )=7.870 E(ELEC)=7.055 | | E(CDIH)=1.947 E(NOE )=8.069 E(PLAN)=2.780 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65633 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65662 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65698 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65690 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65672 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65616 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65486 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65483 intra-atom interactions --------------- step= 12750 at 6.37500 ps -------------------------------- | E(kin)+E(total)=998.768 E(kin)=589.644 temperature=292.193 | | Etotal =409.124 grad(E)=66.735 E(BOND)=219.041 E(ANGL)=381.815 | | E(DIHE)=0.000 E(IMPR)=95.417 E(VDW )=-229.642 E(ELEC)=-135.589 | | E(CDIH)=3.514 E(NOE )=56.829 E(PLAN)=17.739 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.42 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart NBONDS: found 65453 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65442 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65440 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65404 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65354 intra-atom interactions NBONDS: found 65396 intra-atom interactions NBONDS: found 65444 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65534 intra-atom interactions --------------- step= 13000 at 6.50000 ps -------------------------------- | E(kin)+E(total)=999.512 E(kin)=611.924 temperature=303.234 | | Etotal =387.588 grad(E)=66.193 E(BOND)=205.249 E(ANGL)=372.035 | | E(DIHE)=0.000 E(IMPR)=100.316 E(VDW )=-251.309 E(ELEC)=-133.066 | | E(CDIH)=4.648 E(NOE )=66.856 E(PLAN)=22.860 | ------------------------------------------------------------------------------- NBONDS: found 65580 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65632 intra-atom interactions NBONDS: found 65774 intra-atom interactions NBONDS: found 65777 intra-atom interactions NBONDS: found 65711 intra-atom interactions NBONDS: found 65766 intra-atom interactions NBONDS: found 65698 intra-atom interactions --------------- step= 13250 at 6.62500 ps -------------------------------- | E(kin)+E(total)=1004.210 E(kin)=584.279 temperature=289.535 | | Etotal =419.930 grad(E)=68.692 E(BOND)=221.944 E(ANGL)=379.145 | | E(DIHE)=0.000 E(IMPR)=95.796 E(VDW )=-241.367 E(ELEC)=-130.350 | | E(CDIH)=1.399 E(NOE )=72.125 E(PLAN)=21.239 | ------------------------------------------------------------------------------- NBONDS: found 65643 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65696 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65672 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65753 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65779 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65747 intra-atom interactions --------------- step= 13500 at 6.75000 ps -------------------------------- | E(kin)+E(total)=999.122 E(kin)=611.740 temperature=303.143 | | Etotal =387.382 grad(E)=65.040 E(BOND)=199.846 E(ANGL)=369.494 | | E(DIHE)=0.000 E(IMPR)=92.533 E(VDW )=-240.809 E(ELEC)=-130.961 | | E(CDIH)=1.524 E(NOE )=78.862 E(PLAN)=16.892 | ------------------------------------------------------------------------------- %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65715 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 65726 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.43 A apart NBONDS: found 65667 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 65666 intra-atom interactions NBONDS: found 65602 intra-atom interactions NBONDS: found 65671 intra-atom interactions NBONDS: found 65643 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65571 intra-atom interactions --------------- step= 13750 at 6.87500 ps -------------------------------- | E(kin)+E(total)=1006.549 E(kin)=607.484 temperature=301.034 | | Etotal =399.065 grad(E)=68.641 E(BOND)=220.444 E(ANGL)=360.940 | | E(DIHE)=0.000 E(IMPR)=102.631 E(VDW )=-241.117 E(ELEC)=-131.654 | | E(CDIH)=3.142 E(NOE )=67.518 E(PLAN)=17.160 | ------------------------------------------------------------------------------- NBONDS: found 65492 intra-atom interactions NBONDS: found 65400 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65348 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65339 intra-atom interactions NBONDS: found 65411 intra-atom interactions --------------- step= 14000 at 7.00000 ps -------------------------------- | E(kin)+E(total)=1012.823 E(kin)=592.200 temperature=293.460 | | Etotal =420.623 grad(E)=68.209 E(BOND)=218.082 E(ANGL)=395.523 | | E(DIHE)=0.000 E(IMPR)=93.139 E(VDW )=-254.714 E(ELEC)=-132.519 | | E(CDIH)=3.754 E(NOE )=77.887 E(PLAN)=19.470 | ------------------------------------------------------------------------------- NBONDS: found 65422 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65511 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65466 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.42 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart NBONDS: found 65484 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65424 intra-atom interactions --------------- step= 14250 at 7.12500 ps -------------------------------- | E(kin)+E(total)=997.766 E(kin)=594.967 temperature=294.831 | | Etotal =402.798 grad(E)=66.684 E(BOND)=210.355 E(ANGL)=400.332 | | E(DIHE)=0.000 E(IMPR)=93.989 E(VDW )=-257.146 E(ELEC)=-129.871 | | E(CDIH)=3.672 E(NOE )=61.317 E(PLAN)=20.151 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65495 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65499 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65455 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65420 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65391 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65368 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65377 intra-atom interactions --------------- step= 14500 at 7.25000 ps -------------------------------- | E(kin)+E(total)=997.947 E(kin)=595.238 temperature=294.965 | | Etotal =402.709 grad(E)=66.308 E(BOND)=213.951 E(ANGL)=388.005 | | E(DIHE)=0.000 E(IMPR)=96.762 E(VDW )=-252.544 E(ELEC)=-132.898 | | E(CDIH)=3.599 E(NOE )=65.448 E(PLAN)=20.386 | ------------------------------------------------------------------------------- NBONDS: found 65281 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65263 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65258 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65278 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65277 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65283 intra-atom interactions NBONDS: found 65295 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65402 intra-atom interactions --------------- step= 14750 at 7.37500 ps -------------------------------- | E(kin)+E(total)=987.026 E(kin)=586.384 temperature=290.578 | | Etotal =400.642 grad(E)=65.740 E(BOND)=206.651 E(ANGL)=391.635 | | E(DIHE)=0.000 E(IMPR)=93.678 E(VDW )=-261.255 E(ELEC)=-129.864 | | E(CDIH)=1.338 E(NOE )=80.899 E(PLAN)=17.559 | ------------------------------------------------------------------------------- NBONDS: found 65441 intra-atom interactions NBONDS: found 65517 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65741 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65754 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65803 intra-atom interactions NBONDS: found 65852 intra-atom interactions NBONDS: found 65880 intra-atom interactions --------------- step= 15000 at 7.50000 ps -------------------------------- | E(kin)+E(total)=994.745 E(kin)=593.154 temperature=293.933 | | Etotal =401.591 grad(E)=65.589 E(BOND)=205.371 E(ANGL)=399.823 | | E(DIHE)=0.000 E(IMPR)=100.138 E(VDW )=-252.208 E(ELEC)=-132.048 | | E(CDIH)=2.205 E(NOE )=63.571 E(PLAN)=14.737 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=999.707 E(kin)=605.487 temperature=300.044 | | Etotal =394.220 grad(E)=66.761 E(BOND)=216.289 E(ANGL)=373.550 | | E(DIHE)=0.000 E(IMPR)=93.287 E(VDW )=-250.341 E(ELEC)=-133.219 | | E(CDIH)=3.800 E(NOE )=71.811 E(PLAN)=19.042 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.885 E(kin)=12.626 temperature=6.257 | | Etotal =14.953 grad(E)=1.298 E(BOND)=9.961 E(ANGL)=11.034 | | E(DIHE)=0.000 E(IMPR)=6.299 E(VDW )=7.168 E(ELEC)=3.622 | | E(CDIH)=1.772 E(NOE )=7.100 E(PLAN)=2.246 | ------------------------------------------------------------------------------- --------------- averages for last 15000 steps ----------------------------- | E(kin)+E(total)=995.592 E(kin)=605.089 temperature=299.847 | | Etotal =390.503 grad(E)=65.909 E(BOND)=209.825 E(ANGL)=368.447 | | E(DIHE)=0.000 E(IMPR)=93.728 E(VDW )=-249.986 E(ELEC)=-128.689 | | E(CDIH)=3.777 E(NOE )=74.340 E(PLAN)=19.061 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 15000 steps ----------------------- | E(kin)+E(total)=20.554 E(kin)=14.489 temperature=7.180 | | Etotal =19.299 grad(E)=1.824 E(BOND)=11.694 E(ANGL)=13.695 | | E(DIHE)=0.000 E(IMPR)=6.690 E(VDW )=7.759 E(ELEC)=6.912 | | E(CDIH)=1.919 E(NOE )=7.996 E(PLAN)=2.698 | ------------------------------------------------------------------------------- NBONDS: found 65870 intra-atom interactions NBONDS: found 65836 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65864 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65756 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65745 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65694 intra-atom interactions NBONDS: found 65683 intra-atom interactions --------------- step= 15250 at 7.62500 ps -------------------------------- | E(kin)+E(total)=994.866 E(kin)=605.415 temperature=300.008 | | Etotal =389.452 grad(E)=66.733 E(BOND)=223.228 E(ANGL)=373.236 | | E(DIHE)=0.000 E(IMPR)=86.604 E(VDW )=-260.825 E(ELEC)=-129.064 | | E(CDIH)=4.721 E(NOE )=70.772 E(PLAN)=20.780 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.47 A apart NBONDS: found 65686 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65707 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65728 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65781 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65898 intra-atom interactions NBONDS: found 65996 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66017 intra-atom interactions --------------- step= 15500 at 7.75000 ps -------------------------------- | E(kin)+E(total)=997.339 E(kin)=596.470 temperature=295.576 | | Etotal =400.869 grad(E)=68.160 E(BOND)=228.354 E(ANGL)=365.790 | | E(DIHE)=0.000 E(IMPR)=91.174 E(VDW )=-244.262 E(ELEC)=-133.845 | | E(CDIH)=2.607 E(NOE )=67.297 E(PLAN)=23.754 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 66147 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66180 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66184 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65953 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65917 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65865 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65821 intra-atom interactions --------------- step= 15750 at 7.87500 ps -------------------------------- | E(kin)+E(total)=986.815 E(kin)=596.120 temperature=295.403 | | Etotal =390.694 grad(E)=66.589 E(BOND)=223.081 E(ANGL)=362.948 | | E(DIHE)=0.000 E(IMPR)=91.753 E(VDW )=-252.070 E(ELEC)=-127.738 | | E(CDIH)=3.730 E(NOE )=68.853 E(PLAN)=20.137 | ------------------------------------------------------------------------------- %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 65774 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65782 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65738 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65706 intra-atom interactions NBONDS: found 65731 intra-atom interactions NBONDS: found 65763 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.43 A apart NBONDS: found 65778 intra-atom interactions --------------- step= 16000 at 8.00000 ps -------------------------------- | E(kin)+E(total)=988.474 E(kin)=605.029 temperature=299.817 | | Etotal =383.445 grad(E)=67.427 E(BOND)=198.870 E(ANGL)=385.149 | | E(DIHE)=0.000 E(IMPR)=86.414 E(VDW )=-242.295 E(ELEC)=-139.491 | | E(CDIH)=7.043 E(NOE )=71.672 E(PLAN)=16.083 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65811 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65797 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65806 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65807 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65777 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.34 A apart NBONDS: found 65710 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 65621 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65547 intra-atom interactions --------------- step= 16250 at 8.12500 ps -------------------------------- | E(kin)+E(total)=983.976 E(kin)=594.863 temperature=294.780 | | Etotal =389.113 grad(E)=68.073 E(BOND)=209.561 E(ANGL)=384.189 | | E(DIHE)=0.000 E(IMPR)=101.292 E(VDW )=-261.115 E(ELEC)=-130.393 | | E(CDIH)=2.968 E(NOE )=65.248 E(PLAN)=17.361 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65445 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65412 intra-atom interactions NBONDS: found 65368 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65365 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65339 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65417 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65395 intra-atom interactions --------------- step= 16500 at 8.25000 ps -------------------------------- | E(kin)+E(total)=996.160 E(kin)=595.793 temperature=295.240 | | Etotal =400.367 grad(E)=68.041 E(BOND)=219.636 E(ANGL)=361.385 | | E(DIHE)=0.000 E(IMPR)=97.011 E(VDW )=-238.124 E(ELEC)=-138.281 | | E(CDIH)=8.085 E(NOE )=74.717 E(PLAN)=15.938 | ------------------------------------------------------------------------------- NBONDS: found 65364 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65371 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65359 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65375 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65360 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65373 intra-atom interactions NBONDS: found 65342 intra-atom interactions NBONDS: found 65249 intra-atom interactions NBONDS: found 65121 intra-atom interactions --------------- step= 16750 at 8.37500 ps -------------------------------- | E(kin)+E(total)=987.022 E(kin)=597.854 temperature=296.262 | | Etotal =389.168 grad(E)=68.266 E(BOND)=217.340 E(ANGL)=363.868 | | E(DIHE)=0.000 E(IMPR)=98.273 E(VDW )=-246.234 E(ELEC)=-145.367 | | E(CDIH)=6.502 E(NOE )=76.470 E(PLAN)=18.314 | ------------------------------------------------------------------------------- NBONDS: found 65040 intra-atom interactions NBONDS: found 65029 intra-atom interactions NBONDS: found 64945 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 64846 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 64840 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 64807 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 64820 intra-atom interactions --------------- step= 17000 at 8.50000 ps -------------------------------- | E(kin)+E(total)=1003.304 E(kin)=599.311 temperature=296.984 | | Etotal =403.993 grad(E)=66.324 E(BOND)=220.824 E(ANGL)=366.727 | | E(DIHE)=0.000 E(IMPR)=101.393 E(VDW )=-250.002 E(ELEC)=-137.328 | | E(CDIH)=2.312 E(NOE )=83.496 E(PLAN)=16.571 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 64832 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 64865 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 64947 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 64978 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65019 intra-atom interactions NBONDS: found 65118 intra-atom interactions NBONDS: found 65178 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 65263 intra-atom interactions --------------- step= 17250 at 8.62500 ps -------------------------------- | E(kin)+E(total)=999.762 E(kin)=591.169 temperature=292.949 | | Etotal =408.593 grad(E)=67.252 E(BOND)=227.152 E(ANGL)=373.185 | | E(DIHE)=0.000 E(IMPR)=95.857 E(VDW )=-248.463 E(ELEC)=-126.699 | | E(CDIH)=3.462 E(NOE )=65.574 E(PLAN)=18.525 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.41 A apart NBONDS: found 65316 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65372 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65422 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65407 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65422 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65421 intra-atom interactions NBONDS: found 65413 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65427 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65422 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65430 intra-atom interactions --------------- step= 17500 at 8.75000 ps -------------------------------- | E(kin)+E(total)=989.755 E(kin)=590.673 temperature=292.703 | | Etotal =399.082 grad(E)=67.767 E(BOND)=218.922 E(ANGL)=364.022 | | E(DIHE)=0.000 E(IMPR)=100.110 E(VDW )=-253.275 E(ELEC)=-129.156 | | E(CDIH)=4.035 E(NOE )=78.119 E(PLAN)=16.306 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=995.894 E(kin)=605.495 temperature=300.048 | | Etotal =390.399 grad(E)=67.408 E(BOND)=215.707 E(ANGL)=369.569 | | E(DIHE)=0.000 E(IMPR)=94.156 E(VDW )=-249.572 E(ELEC)=-133.970 | | E(CDIH)=3.810 E(NOE )=71.655 E(PLAN)=19.043 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.972 E(kin)=12.423 temperature=6.156 | | Etotal =15.498 grad(E)=1.461 E(BOND)=10.175 E(ANGL)=12.460 | | E(DIHE)=0.000 E(IMPR)=6.379 E(VDW )=7.942 E(ELEC)=6.107 | | E(CDIH)=1.816 E(NOE )=6.965 E(PLAN)=2.645 | ------------------------------------------------------------------------------- --------------- averages for last 17500 steps ----------------------------- | E(kin)+E(total)=995.635 E(kin)=605.147 temperature=299.876 | | Etotal =390.488 grad(E)=66.123 E(BOND)=210.666 E(ANGL)=368.607 | | E(DIHE)=0.000 E(IMPR)=93.789 E(VDW )=-249.927 E(ELEC)=-129.443 | | E(CDIH)=3.781 E(NOE )=73.956 E(PLAN)=19.058 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 17500 steps ----------------------- | E(kin)+E(total)=19.399 E(kin)=14.213 temperature=7.043 | | Etotal =18.804 grad(E)=1.853 E(BOND)=11.672 E(ANGL)=13.531 | | E(DIHE)=0.000 E(IMPR)=6.648 E(VDW )=7.787 E(ELEC)=7.049 | | E(CDIH)=1.905 E(NOE )=7.913 E(PLAN)=2.691 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65487 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65513 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65583 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65623 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65629 intra-atom interactions NBONDS: found 65596 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65590 intra-atom interactions NBONDS: found 65671 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65624 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65648 intra-atom interactions --------------- step= 17750 at 8.87500 ps -------------------------------- | E(kin)+E(total)=989.918 E(kin)=616.739 temperature=305.620 | | Etotal =373.179 grad(E)=67.485 E(BOND)=214.487 E(ANGL)=355.409 | | E(DIHE)=0.000 E(IMPR)=85.876 E(VDW )=-248.289 E(ELEC)=-135.636 | | E(CDIH)=3.336 E(NOE )=80.607 E(PLAN)=17.388 | ------------------------------------------------------------------------------- NBONDS: found 65669 intra-atom interactions NBONDS: found 65692 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65779 intra-atom interactions NBONDS: found 65802 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65814 intra-atom interactions NBONDS: found 65901 intra-atom interactions NBONDS: found 65924 intra-atom interactions NBONDS: found 65931 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65922 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65979 intra-atom interactions NBONDS: found 65999 intra-atom interactions --------------- step= 18000 at 9.00000 ps -------------------------------- | E(kin)+E(total)=993.436 E(kin)=619.845 temperature=307.159 | | Etotal =373.590 grad(E)=67.595 E(BOND)=206.821 E(ANGL)=375.143 | | E(DIHE)=0.000 E(IMPR)=80.558 E(VDW )=-248.859 E(ELEC)=-134.822 | | E(CDIH)=3.480 E(NOE )=70.172 E(PLAN)=21.097 | ------------------------------------------------------------------------------- NBONDS: found 65997 intra-atom interactions NBONDS: found 66017 intra-atom interactions NBONDS: found 66009 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66003 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66002 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65959 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65951 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65951 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65917 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65898 intra-atom interactions NBONDS: found 65907 intra-atom interactions NBONDS: found 65951 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66010 intra-atom interactions --------------- step= 18250 at 9.12500 ps -------------------------------- | E(kin)+E(total)=1002.358 E(kin)=612.656 temperature=303.597 | | Etotal =389.701 grad(E)=69.167 E(BOND)=208.803 E(ANGL)=368.110 | | E(DIHE)=0.000 E(IMPR)=102.658 E(VDW )=-257.739 E(ELEC)=-127.780 | | E(CDIH)=1.911 E(NOE )=73.889 E(PLAN)=19.850 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65976 intra-atom interactions NBONDS: found 65997 intra-atom interactions NBONDS: found 66018 intra-atom interactions NBONDS: found 66025 intra-atom interactions NBONDS: found 65981 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65957 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65970 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65908 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 65817 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65777 intra-atom interactions --------------- step= 18500 at 9.25000 ps -------------------------------- | E(kin)+E(total)=999.959 E(kin)=618.127 temperature=306.308 | | Etotal =381.832 grad(E)=66.930 E(BOND)=197.608 E(ANGL)=375.786 | | E(DIHE)=0.000 E(IMPR)=95.760 E(VDW )=-242.633 E(ELEC)=-139.599 | | E(CDIH)=5.661 E(NOE )=68.001 E(PLAN)=21.248 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65767 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65751 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65696 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65707 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65702 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65673 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65699 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65689 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65710 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65587 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65572 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65538 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65515 intra-atom interactions --------------- step= 18750 at 9.37500 ps -------------------------------- | E(kin)+E(total)=994.034 E(kin)=590.818 temperature=292.775 | | Etotal =403.216 grad(E)=68.297 E(BOND)=223.036 E(ANGL)=380.657 | | E(DIHE)=0.000 E(IMPR)=86.405 E(VDW )=-250.270 E(ELEC)=-139.728 | | E(CDIH)=3.053 E(NOE )=79.095 E(PLAN)=20.968 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65508 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65499 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65482 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65502 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65551 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65561 intra-atom interactions NBONDS: found 65602 intra-atom interactions NBONDS: found 65632 intra-atom interactions NBONDS: found 65648 intra-atom interactions NBONDS: found 65641 intra-atom interactions NBONDS: found 65706 intra-atom interactions NBONDS: found 65751 intra-atom interactions NBONDS: found 65783 intra-atom interactions NBONDS: found 65809 intra-atom interactions NBONDS: found 65807 intra-atom interactions --------------- step= 19000 at 9.50000 ps -------------------------------- | E(kin)+E(total)=998.952 E(kin)=626.441 temperature=310.428 | | Etotal =372.510 grad(E)=65.244 E(BOND)=211.882 E(ANGL)=348.651 | | E(DIHE)=0.000 E(IMPR)=95.082 E(VDW )=-237.149 E(ELEC)=-136.652 | | E(CDIH)=4.317 E(NOE )=67.697 E(PLAN)=18.683 | ------------------------------------------------------------------------------- NBONDS: found 65843 intra-atom interactions NBONDS: found 65846 intra-atom interactions NBONDS: found 65793 intra-atom interactions NBONDS: found 65833 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65845 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65805 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65799 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65738 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.41 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65670 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65588 intra-atom interactions --------------- step= 19250 at 9.62500 ps -------------------------------- | E(kin)+E(total)=980.615 E(kin)=603.747 temperature=299.182 | | Etotal =376.867 grad(E)=67.093 E(BOND)=212.283 E(ANGL)=372.642 | | E(DIHE)=0.000 E(IMPR)=87.378 E(VDW )=-249.712 E(ELEC)=-134.478 | | E(CDIH)=2.307 E(NOE )=66.344 E(PLAN)=20.104 | ------------------------------------------------------------------------------- NBONDS: found 65518 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65466 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65440 intra-atom interactions NBONDS: found 65447 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65403 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65405 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65440 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65523 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65524 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65570 intra-atom interactions --------------- step= 19500 at 9.75000 ps -------------------------------- | E(kin)+E(total)=986.929 E(kin)=600.488 temperature=297.567 | | Etotal =386.441 grad(E)=66.658 E(BOND)=225.512 E(ANGL)=378.192 | | E(DIHE)=0.000 E(IMPR)=80.637 E(VDW )=-256.228 E(ELEC)=-144.569 | | E(CDIH)=5.739 E(NOE )=81.297 E(PLAN)=15.859 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65535 intra-atom interactions NBONDS: found 65528 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65492 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65430 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65373 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.39 A apart NBONDS: found 65267 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65219 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65174 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65132 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 65077 intra-atom interactions --------------- step= 19750 at 9.87500 ps -------------------------------- | E(kin)+E(total)=974.717 E(kin)=614.545 temperature=304.533 | | Etotal =360.173 grad(E)=65.146 E(BOND)=208.694 E(ANGL)=355.439 | | E(DIHE)=0.000 E(IMPR)=102.856 E(VDW )=-251.454 E(ELEC)=-139.070 | | E(CDIH)=5.145 E(NOE )=57.375 E(PLAN)=21.188 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65074 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65090 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65103 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65197 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65228 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65305 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65290 intra-atom interactions --------------- step= 20000 at 10.00000 ps -------------------------------- | E(kin)+E(total)=1003.421 E(kin)=590.323 temperature=292.530 | | Etotal =413.097 grad(E)=68.273 E(BOND)=223.338 E(ANGL)=363.219 | | E(DIHE)=0.000 E(IMPR)=102.286 E(VDW )=-248.490 E(ELEC)=-134.471 | | E(CDIH)=2.702 E(NOE )=80.375 E(PLAN)=24.138 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=994.283 E(kin)=605.430 temperature=300.016 | | Etotal =388.853 grad(E)=67.456 E(BOND)=213.538 E(ANGL)=370.816 | | E(DIHE)=0.000 E(IMPR)=96.510 E(VDW )=-251.071 E(ELEC)=-135.719 | | E(CDIH)=3.686 E(NOE )=72.143 E(PLAN)=18.950 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.240 E(kin)=12.322 temperature=6.106 | | Etotal =14.974 grad(E)=1.473 E(BOND)=9.814 E(ANGL)=12.644 | | E(DIHE)=0.000 E(IMPR)=6.979 E(VDW )=6.694 E(ELEC)=4.539 | | E(CDIH)=1.797 E(NOE )=6.905 E(PLAN)=2.550 | ------------------------------------------------------------------------------- --------------- averages for last 20000 steps ----------------------------- | E(kin)+E(total)=995.466 E(kin)=605.183 temperature=299.893 | | Etotal =390.283 grad(E)=66.290 E(BOND)=211.025 E(ANGL)=368.883 | | E(DIHE)=0.000 E(IMPR)=94.129 E(VDW )=-250.070 E(ELEC)=-130.228 | | E(CDIH)=3.769 E(NOE )=73.729 E(PLAN)=19.045 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20000 steps ----------------------- | E(kin)+E(total)=18.443 E(kin)=13.991 temperature=6.933 | | Etotal =18.377 grad(E)=1.862 E(BOND)=11.496 E(ANGL)=13.443 | | E(DIHE)=0.000 E(IMPR)=6.751 E(VDW )=7.668 E(ELEC)=7.097 | | E(CDIH)=1.892 E(NOE )=7.817 E(PLAN)=2.674 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65333 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65352 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65350 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65322 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65346 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65329 intra-atom interactions --------------- step= 20250 at 10.12500 ps -------------------------------- | E(kin)+E(total)=991.840 E(kin)=604.839 temperature=299.723 | | Etotal =387.000 grad(E)=66.741 E(BOND)=213.446 E(ANGL)=378.740 | | E(DIHE)=0.000 E(IMPR)=87.229 E(VDW )=-239.076 E(ELEC)=-135.332 | | E(CDIH)=1.433 E(NOE )=61.338 E(PLAN)=19.223 | ------------------------------------------------------------------------------- NBONDS: found 65344 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65281 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65282 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65261 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart NBONDS: found 65315 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65403 intra-atom interactions --------------- step= 20500 at 10.25000 ps -------------------------------- | E(kin)+E(total)=1004.556 E(kin)=612.358 temperature=303.449 | | Etotal =392.197 grad(E)=66.756 E(BOND)=226.446 E(ANGL)=370.782 | | E(DIHE)=0.000 E(IMPR)=84.002 E(VDW )=-242.208 E(ELEC)=-137.335 | | E(CDIH)=1.073 E(NOE )=70.771 E(PLAN)=18.667 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65457 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65530 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65648 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65715 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65864 intra-atom interactions NBONDS: found 65787 intra-atom interactions NBONDS: found 65789 intra-atom interactions --------------- step= 20750 at 10.37500 ps -------------------------------- | E(kin)+E(total)=994.594 E(kin)=614.560 temperature=304.540 | | Etotal =380.034 grad(E)=65.250 E(BOND)=229.976 E(ANGL)=367.273 | | E(DIHE)=0.000 E(IMPR)=82.557 E(VDW )=-247.259 E(ELEC)=-137.822 | | E(CDIH)=3.173 E(NOE )=64.032 E(PLAN)=18.105 | ------------------------------------------------------------------------------- NBONDS: found 65843 intra-atom interactions NBONDS: found 65772 intra-atom interactions NBONDS: found 65693 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65588 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65585 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65550 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 65566 intra-atom interactions --------------- step= 21000 at 10.50000 ps -------------------------------- | E(kin)+E(total)=999.338 E(kin)=626.262 temperature=310.339 | | Etotal =373.076 grad(E)=65.561 E(BOND)=211.936 E(ANGL)=357.476 | | E(DIHE)=0.000 E(IMPR)=90.131 E(VDW )=-259.319 E(ELEC)=-128.488 | | E(CDIH)=2.691 E(NOE )=79.493 E(PLAN)=19.156 | ------------------------------------------------------------------------------- NBONDS: found 65587 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65682 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65747 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65855 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65904 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65940 intra-atom interactions NBONDS: found 65942 intra-atom interactions --------------- step= 21250 at 10.62500 ps -------------------------------- | E(kin)+E(total)=977.167 E(kin)=609.941 temperature=302.251 | | Etotal =367.225 grad(E)=66.605 E(BOND)=216.034 E(ANGL)=357.791 | | E(DIHE)=0.000 E(IMPR)=95.583 E(VDW )=-249.732 E(ELEC)=-143.113 | | E(CDIH)=5.822 E(NOE )=67.488 E(PLAN)=17.353 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65943 intra-atom interactions NBONDS: found 65932 intra-atom interactions NBONDS: found 65960 intra-atom interactions NBONDS: found 65955 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65952 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65914 intra-atom interactions NBONDS: found 65889 intra-atom interactions --------------- step= 21500 at 10.75000 ps -------------------------------- | E(kin)+E(total)=996.094 E(kin)=618.471 temperature=306.478 | | Etotal =377.623 grad(E)=66.511 E(BOND)=217.555 E(ANGL)=344.511 | | E(DIHE)=0.000 E(IMPR)=112.200 E(VDW )=-255.778 E(ELEC)=-124.662 | | E(CDIH)=0.675 E(NOE )=66.401 E(PLAN)=16.721 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65918 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65932 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 65905 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.37 A apart NBONDS: found 65921 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65976 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65998 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65967 intra-atom interactions --------------- step= 21750 at 10.87500 ps -------------------------------- | E(kin)+E(total)=980.040 E(kin)=624.971 temperature=309.700 | | Etotal =355.069 grad(E)=66.419 E(BOND)=214.438 E(ANGL)=337.913 | | E(DIHE)=0.000 E(IMPR)=98.408 E(VDW )=-253.947 E(ELEC)=-127.005 | | E(CDIH)=2.896 E(NOE )=63.980 E(PLAN)=18.386 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66021 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66099 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66141 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66231 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66221 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 66203 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66145 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 66090 intra-atom interactions --------------- step= 22000 at 11.00000 ps -------------------------------- | E(kin)+E(total)=997.470 E(kin)=605.800 temperature=300.200 | | Etotal =391.670 grad(E)=67.808 E(BOND)=223.084 E(ANGL)=374.174 | | E(DIHE)=0.000 E(IMPR)=97.612 E(VDW )=-258.860 E(ELEC)=-139.922 | | E(CDIH)=6.571 E(NOE )=71.691 E(PLAN)=17.319 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66049 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66058 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 66067 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66085 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66142 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66147 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66189 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66198 intra-atom interactions --------------- step= 22250 at 11.12500 ps -------------------------------- | E(kin)+E(total)=988.785 E(kin)=618.840 temperature=306.661 | | Etotal =369.945 grad(E)=66.843 E(BOND)=199.757 E(ANGL)=364.807 | | E(DIHE)=0.000 E(IMPR)=94.535 E(VDW )=-246.108 E(ELEC)=-128.965 | | E(CDIH)=3.284 E(NOE )=61.737 E(PLAN)=20.898 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66215 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66213 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66207 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66191 intra-atom interactions NBONDS: found 66160 intra-atom interactions NBONDS: found 66081 intra-atom interactions NBONDS: found 66087 intra-atom interactions --------------- step= 22500 at 11.25000 ps -------------------------------- | E(kin)+E(total)=997.281 E(kin)=595.326 temperature=295.009 | | Etotal =401.956 grad(E)=69.287 E(BOND)=214.563 E(ANGL)=373.067 | | E(DIHE)=0.000 E(IMPR)=104.508 E(VDW )=-256.494 E(ELEC)=-129.219 | | E(CDIH)=2.937 E(NOE )=73.362 E(PLAN)=19.232 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=996.075 E(kin)=605.514 temperature=300.058 | | Etotal =390.561 grad(E)=67.034 E(BOND)=218.239 E(ANGL)=367.512 | | E(DIHE)=0.000 E(IMPR)=95.600 E(VDW )=-250.913 E(ELEC)=-133.539 | | E(CDIH)=3.694 E(NOE )=70.544 E(PLAN)=19.424 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.971 E(kin)=13.127 temperature=6.505 | | Etotal =14.839 grad(E)=1.404 E(BOND)=10.262 E(ANGL)=11.524 | | E(DIHE)=0.000 E(IMPR)=6.982 E(VDW )=6.915 E(ELEC)=5.213 | | E(CDIH)=1.686 E(NOE )=7.427 E(PLAN)=2.030 | ------------------------------------------------------------------------------- --------------- averages for last 22500 steps ----------------------------- | E(kin)+E(total)=995.534 E(kin)=605.220 temperature=299.912 | | Etotal =390.314 grad(E)=66.372 E(BOND)=211.826 E(ANGL)=368.731 | | E(DIHE)=0.000 E(IMPR)=94.293 E(VDW )=-250.164 E(ELEC)=-130.596 | | E(CDIH)=3.761 E(NOE )=73.375 E(PLAN)=19.087 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 22500 steps ----------------------- | E(kin)+E(total)=17.591 E(kin)=13.898 temperature=6.887 | | Etotal =18.018 grad(E)=1.832 E(BOND)=11.589 E(ANGL)=13.251 | | E(DIHE)=0.000 E(IMPR)=6.793 E(VDW )=7.593 E(ELEC)=6.991 | | E(CDIH)=1.870 E(NOE )=7.839 E(PLAN)=2.613 | ------------------------------------------------------------------------------- NBONDS: found 66057 intra-atom interactions NBONDS: found 66112 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66057 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66000 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65979 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65913 intra-atom interactions --------------- step= 22750 at 11.37500 ps -------------------------------- | E(kin)+E(total)=993.150 E(kin)=636.591 temperature=315.458 | | Etotal =356.559 grad(E)=65.050 E(BOND)=215.536 E(ANGL)=341.053 | | E(DIHE)=0.000 E(IMPR)=93.538 E(VDW )=-246.945 E(ELEC)=-139.372 | | E(CDIH)=5.998 E(NOE )=68.007 E(PLAN)=18.746 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65918 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65938 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65888 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65925 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65855 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65887 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65952 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65975 intra-atom interactions --------------- step= 23000 at 11.50000 ps -------------------------------- | E(kin)+E(total)=994.237 E(kin)=602.021 temperature=298.327 | | Etotal =392.217 grad(E)=66.591 E(BOND)=217.597 E(ANGL)=373.887 | | E(DIHE)=0.000 E(IMPR)=84.932 E(VDW )=-245.310 E(ELEC)=-135.527 | | E(CDIH)=7.185 E(NOE )=69.921 E(PLAN)=19.531 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66065 intra-atom interactions NBONDS: found 66101 intra-atom interactions NBONDS: found 66137 intra-atom interactions NBONDS: found 66218 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66205 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 66173 intra-atom interactions --------------- step= 23250 at 11.62500 ps -------------------------------- | E(kin)+E(total)=998.100 E(kin)=596.541 temperature=295.611 | | Etotal =401.559 grad(E)=66.475 E(BOND)=229.476 E(ANGL)=367.138 | | E(DIHE)=0.000 E(IMPR)=95.183 E(VDW )=-257.325 E(ELEC)=-133.784 | | E(CDIH)=0.950 E(NOE )=79.683 E(PLAN)=20.238 | ------------------------------------------------------------------------------- %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 66180 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66147 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66137 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66206 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 66282 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66327 intra-atom interactions --------------- step= 23500 at 11.75000 ps -------------------------------- | E(kin)+E(total)=996.393 E(kin)=631.906 temperature=313.136 | | Etotal =364.487 grad(E)=65.507 E(BOND)=204.375 E(ANGL)=355.148 | | E(DIHE)=0.000 E(IMPR)=94.527 E(VDW )=-246.523 E(ELEC)=-141.234 | | E(CDIH)=2.661 E(NOE )=74.484 E(PLAN)=21.049 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 66545 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66632 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.45 A apart NBONDS: found 66677 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66751 intra-atom interactions NBONDS: found 66804 intra-atom interactions NBONDS: found 66791 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66818 intra-atom interactions --------------- step= 23750 at 11.87500 ps -------------------------------- | E(kin)+E(total)=1004.386 E(kin)=604.216 temperature=299.414 | | Etotal =400.170 grad(E)=67.425 E(BOND)=217.029 E(ANGL)=376.100 | | E(DIHE)=0.000 E(IMPR)=102.072 E(VDW )=-246.850 E(ELEC)=-138.549 | | E(CDIH)=4.152 E(NOE )=70.454 E(PLAN)=15.761 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66782 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66683 intra-atom interactions NBONDS: found 66680 intra-atom interactions NBONDS: found 66586 intra-atom interactions NBONDS: found 66596 intra-atom interactions NBONDS: found 66628 intra-atom interactions NBONDS: found 66646 intra-atom interactions --------------- step= 24000 at 12.00000 ps -------------------------------- | E(kin)+E(total)=986.503 E(kin)=605.642 temperature=300.121 | | Etotal =380.861 grad(E)=66.843 E(BOND)=190.388 E(ANGL)=384.227 | | E(DIHE)=0.000 E(IMPR)=95.917 E(VDW )=-248.940 E(ELEC)=-132.894 | | E(CDIH)=2.111 E(NOE )=69.803 E(PLAN)=20.250 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66641 intra-atom interactions NBONDS: found 66680 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66675 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 66703 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 66649 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66631 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 66590 intra-atom interactions NBONDS: found 66516 intra-atom interactions --------------- step= 24250 at 12.12500 ps -------------------------------- | E(kin)+E(total)=983.877 E(kin)=618.234 temperature=306.361 | | Etotal =365.642 grad(E)=66.029 E(BOND)=206.174 E(ANGL)=360.658 | | E(DIHE)=0.000 E(IMPR)=95.853 E(VDW )=-248.401 E(ELEC)=-136.578 | | E(CDIH)=2.973 E(NOE )=64.862 E(PLAN)=20.101 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66487 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66465 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 66464 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66435 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66331 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66262 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66152 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66102 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 66066 intra-atom interactions --------------- step= 24500 at 12.25000 ps -------------------------------- | E(kin)+E(total)=1002.241 E(kin)=585.171 temperature=289.977 | | Etotal =417.070 grad(E)=69.188 E(BOND)=204.374 E(ANGL)=399.105 | | E(DIHE)=0.000 E(IMPR)=96.973 E(VDW )=-250.268 E(ELEC)=-132.642 | | E(CDIH)=4.345 E(NOE )=75.181 E(PLAN)=20.002 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 66024 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65978 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65968 intra-atom interactions NBONDS: found 65980 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65954 intra-atom interactions NBONDS: found 65932 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65930 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65903 intra-atom interactions --------------- step= 24750 at 12.37500 ps -------------------------------- | E(kin)+E(total)=984.243 E(kin)=619.602 temperature=307.039 | | Etotal =364.641 grad(E)=64.700 E(BOND)=220.626 E(ANGL)=347.858 | | E(DIHE)=0.000 E(IMPR)=91.141 E(VDW )=-256.843 E(ELEC)=-123.615 | | E(CDIH)=2.284 E(NOE )=65.336 E(PLAN)=17.854 | ------------------------------------------------------------------------------- NBONDS: found 65944 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65909 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65862 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65864 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65882 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65840 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65723 intra-atom interactions NBONDS: found 65662 intra-atom interactions NBONDS: found 65651 intra-atom interactions --------------- step= 25000 at 12.50000 ps -------------------------------- | E(kin)+E(total)=992.315 E(kin)=603.566 temperature=299.092 | | Etotal =388.749 grad(E)=66.222 E(BOND)=209.713 E(ANGL)=356.313 | | E(DIHE)=0.000 E(IMPR)=105.536 E(VDW )=-256.244 E(ELEC)=-128.520 | | E(CDIH)=3.889 E(NOE )=75.554 E(PLAN)=22.508 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=995.618 E(kin)=605.496 temperature=300.049 | | Etotal =390.123 grad(E)=66.406 E(BOND)=217.976 E(ANGL)=368.387 | | E(DIHE)=0.000 E(IMPR)=94.570 E(VDW )=-251.637 E(ELEC)=-133.981 | | E(CDIH)=3.393 E(NOE )=71.801 E(PLAN)=19.614 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.002 E(kin)=12.378 temperature=6.134 | | Etotal =14.281 grad(E)=1.316 E(BOND)=9.682 E(ANGL)=12.305 | | E(DIHE)=0.000 E(IMPR)=6.187 E(VDW )=5.961 E(ELEC)=4.278 | | E(CDIH)=1.716 E(NOE )=6.198 E(PLAN)=2.400 | ------------------------------------------------------------------------------- --------------- averages for last 25000 steps ----------------------------- | E(kin)+E(total)=995.542 E(kin)=605.247 temperature=299.925 | | Etotal =390.295 grad(E)=66.376 E(BOND)=212.441 E(ANGL)=368.697 | | E(DIHE)=0.000 E(IMPR)=94.320 E(VDW )=-250.311 E(ELEC)=-130.934 | | E(CDIH)=3.724 E(NOE )=73.218 E(PLAN)=19.140 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 25000 steps ----------------------- | E(kin)+E(total)=16.879 E(kin)=13.754 temperature=6.815 | | Etotal =17.680 grad(E)=1.787 E(BOND)=11.561 E(ANGL)=13.160 | | E(DIHE)=0.000 E(IMPR)=6.735 E(VDW )=7.459 E(ELEC)=6.844 | | E(CDIH)=1.859 E(NOE )=7.705 E(PLAN)=2.597 | ------------------------------------------------------------------------------- NBONDS: found 65647 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65623 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65644 intra-atom interactions NBONDS: found 65670 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65670 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65713 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65720 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65780 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65780 intra-atom interactions --------------- step= 25250 at 12.62500 ps -------------------------------- | E(kin)+E(total)=992.756 E(kin)=597.954 temperature=296.312 | | Etotal =394.801 grad(E)=66.881 E(BOND)=223.359 E(ANGL)=361.541 | | E(DIHE)=0.000 E(IMPR)=96.032 E(VDW )=-251.946 E(ELEC)=-132.676 | | E(CDIH)=1.233 E(NOE )=82.858 E(PLAN)=14.400 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65815 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65853 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65927 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65925 intra-atom interactions NBONDS: found 65924 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65905 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65961 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65916 intra-atom interactions --------------- step= 25500 at 12.75000 ps -------------------------------- | E(kin)+E(total)=989.491 E(kin)=587.747 temperature=291.253 | | Etotal =401.744 grad(E)=64.735 E(BOND)=213.486 E(ANGL)=382.905 | | E(DIHE)=0.000 E(IMPR)=94.664 E(VDW )=-258.290 E(ELEC)=-125.783 | | E(CDIH)=4.089 E(NOE )=72.570 E(PLAN)=18.103 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.34 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65904 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65867 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65826 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65834 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65802 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65813 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65838 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 65854 intra-atom interactions --------------- step= 25750 at 12.87500 ps -------------------------------- | E(kin)+E(total)=1000.430 E(kin)=608.010 temperature=301.295 | | Etotal =392.420 grad(E)=65.124 E(BOND)=210.032 E(ANGL)=359.654 | | E(DIHE)=0.000 E(IMPR)=99.854 E(VDW )=-253.094 E(ELEC)=-131.019 | | E(CDIH)=8.045 E(NOE )=78.556 E(PLAN)=20.392 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 65866 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 65906 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65870 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 65819 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65842 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65861 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65861 intra-atom interactions --------------- step= 26000 at 13.00000 ps -------------------------------- | E(kin)+E(total)=996.656 E(kin)=605.295 temperature=299.949 | | Etotal =391.361 grad(E)=67.219 E(BOND)=211.575 E(ANGL)=357.605 | | E(DIHE)=0.000 E(IMPR)=105.394 E(VDW )=-240.376 E(ELEC)=-134.998 | | E(CDIH)=5.388 E(NOE )=69.488 E(PLAN)=17.284 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65797 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65738 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65618 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65565 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65458 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65379 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65324 intra-atom interactions --------------- step= 26250 at 13.12500 ps -------------------------------- | E(kin)+E(total)=1016.343 E(kin)=609.798 temperature=302.180 | | Etotal =406.545 grad(E)=66.060 E(BOND)=208.920 E(ANGL)=372.599 | | E(DIHE)=0.000 E(IMPR)=92.126 E(VDW )=-257.065 E(ELEC)=-116.321 | | E(CDIH)=8.180 E(NOE )=80.825 E(PLAN)=17.281 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65431 intra-atom interactions NBONDS: found 65560 intra-atom interactions NBONDS: found 65676 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65772 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65795 intra-atom interactions NBONDS: found 65820 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65838 intra-atom interactions NBONDS: found 65867 intra-atom interactions --------------- step= 26500 at 13.25000 ps -------------------------------- | E(kin)+E(total)=1005.139 E(kin)=592.854 temperature=293.784 | | Etotal =412.285 grad(E)=67.281 E(BOND)=220.367 E(ANGL)=373.747 | | E(DIHE)=0.000 E(IMPR)=112.861 E(VDW )=-256.091 E(ELEC)=-130.968 | | E(CDIH)=3.539 E(NOE )=72.448 E(PLAN)=16.382 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65835 intra-atom interactions NBONDS: found 65793 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65844 intra-atom interactions NBONDS: found 65812 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65831 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65847 intra-atom interactions NBONDS: found 65793 intra-atom interactions NBONDS: found 65782 intra-atom interactions --------------- step= 26750 at 13.37500 ps -------------------------------- | E(kin)+E(total)=1010.038 E(kin)=595.703 temperature=295.196 | | Etotal =414.335 grad(E)=66.878 E(BOND)=218.605 E(ANGL)=375.897 | | E(DIHE)=0.000 E(IMPR)=107.219 E(VDW )=-245.889 E(ELEC)=-127.765 | | E(CDIH)=1.727 E(NOE )=64.147 E(PLAN)=20.393 | ------------------------------------------------------------------------------- NBONDS: found 65764 intra-atom interactions NBONDS: found 65792 intra-atom interactions NBONDS: found 65863 intra-atom interactions NBONDS: found 65808 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65848 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65904 intra-atom interactions NBONDS: found 65978 intra-atom interactions NBONDS: found 66075 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66121 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 66099 intra-atom interactions --------------- step= 27000 at 13.50000 ps -------------------------------- | E(kin)+E(total)=995.800 E(kin)=589.747 temperature=292.244 | | Etotal =406.053 grad(E)=67.029 E(BOND)=219.254 E(ANGL)=373.528 | | E(DIHE)=0.000 E(IMPR)=95.683 E(VDW )=-252.567 E(ELEC)=-137.212 | | E(CDIH)=2.563 E(NOE )=81.310 E(PLAN)=23.495 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 66089 intra-atom interactions NBONDS: found 66120 intra-atom interactions NBONDS: found 66206 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66082 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66024 intra-atom interactions NBONDS: found 65983 intra-atom interactions NBONDS: found 65965 intra-atom interactions --------------- step= 27250 at 13.62500 ps -------------------------------- | E(kin)+E(total)=976.770 E(kin)=588.592 temperature=291.672 | | Etotal =388.178 grad(E)=66.198 E(BOND)=210.219 E(ANGL)=378.825 | | E(DIHE)=0.000 E(IMPR)=106.192 E(VDW )=-256.145 E(ELEC)=-131.062 | | E(CDIH)=1.390 E(NOE )=58.082 E(PLAN)=20.677 | ------------------------------------------------------------------------------- NBONDS: found 65847 intra-atom interactions NBONDS: found 65907 intra-atom interactions NBONDS: found 65906 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65953 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65955 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65998 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.48 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 65942 intra-atom interactions --------------- step= 27500 at 13.75000 ps -------------------------------- | E(kin)+E(total)=990.755 E(kin)=604.546 temperature=299.578 | | Etotal =386.209 grad(E)=68.004 E(BOND)=212.469 E(ANGL)=369.274 | | E(DIHE)=0.000 E(IMPR)=98.169 E(VDW )=-257.112 E(ELEC)=-127.336 | | E(CDIH)=4.135 E(NOE )=69.365 E(PLAN)=17.245 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=995.443 E(kin)=605.491 temperature=300.046 | | Etotal =389.952 grad(E)=66.535 E(BOND)=213.210 E(ANGL)=368.278 | | E(DIHE)=0.000 E(IMPR)=96.555 E(VDW )=-253.411 E(ELEC)=-129.943 | | E(CDIH)=3.642 E(NOE )=72.436 E(PLAN)=19.185 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.108 E(kin)=13.310 temperature=6.596 | | Etotal =15.009 grad(E)=1.327 E(BOND)=9.858 E(ANGL)=12.382 | | E(DIHE)=0.000 E(IMPR)=6.702 E(VDW )=7.228 E(ELEC)=4.790 | | E(CDIH)=1.852 E(NOE )=6.863 E(PLAN)=2.373 | ------------------------------------------------------------------------------- --------------- averages for last 27500 steps ----------------------------- | E(kin)+E(total)=995.533 E(kin)=605.269 temperature=299.936 | | Etotal =390.264 grad(E)=66.390 E(BOND)=212.511 E(ANGL)=368.658 | | E(DIHE)=0.000 E(IMPR)=94.523 E(VDW )=-250.593 E(ELEC)=-130.844 | | E(CDIH)=3.717 E(NOE )=73.147 E(PLAN)=19.144 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 27500 steps ----------------------- | E(kin)+E(total)=16.278 E(kin)=13.714 temperature=6.796 | | Etotal =17.454 grad(E)=1.751 E(BOND)=11.419 E(ANGL)=13.091 | | E(DIHE)=0.000 E(IMPR)=6.763 E(VDW )=7.491 E(ELEC)=6.690 | | E(CDIH)=1.858 E(NOE )=7.636 E(PLAN)=2.578 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65905 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65895 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65853 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65913 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65930 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 66013 intra-atom interactions --------------- step= 27750 at 13.87500 ps -------------------------------- | E(kin)+E(total)=1008.566 E(kin)=599.048 temperature=296.853 | | Etotal =409.518 grad(E)=67.064 E(BOND)=229.513 E(ANGL)=360.531 | | E(DIHE)=0.000 E(IMPR)=97.144 E(VDW )=-245.590 E(ELEC)=-124.987 | | E(CDIH)=4.966 E(NOE )=67.215 E(PLAN)=20.725 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart NBONDS: found 66064 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart NBONDS: found 66019 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65913 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.48 A apart NBONDS: found 65829 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65788 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65764 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65794 intra-atom interactions --------------- step= 28000 at 14.00000 ps -------------------------------- | E(kin)+E(total)=1014.774 E(kin)=597.774 temperature=296.222 | | Etotal =417.000 grad(E)=68.892 E(BOND)=222.995 E(ANGL)=378.336 | | E(DIHE)=0.000 E(IMPR)=112.975 E(VDW )=-256.745 E(ELEC)=-133.664 | | E(CDIH)=5.595 E(NOE )=73.536 E(PLAN)=13.973 | ------------------------------------------------------------------------------- NBONDS: found 65780 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65811 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65784 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65765 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65826 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65787 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65827 intra-atom interactions --------------- step= 28250 at 14.12500 ps -------------------------------- | E(kin)+E(total)=997.957 E(kin)=595.261 temperature=294.977 | | Etotal =402.696 grad(E)=68.869 E(BOND)=219.252 E(ANGL)=378.027 | | E(DIHE)=0.000 E(IMPR)=99.822 E(VDW )=-239.956 E(ELEC)=-141.817 | | E(CDIH)=2.792 E(NOE )=64.245 E(PLAN)=20.331 | ------------------------------------------------------------------------------- NBONDS: found 65824 intra-atom interactions NBONDS: found 65807 intra-atom interactions NBONDS: found 65827 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65920 intra-atom interactions NBONDS: found 66014 intra-atom interactions NBONDS: found 65999 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66026 intra-atom interactions --------------- step= 28500 at 14.25000 ps -------------------------------- | E(kin)+E(total)=988.102 E(kin)=608.258 temperature=301.417 | | Etotal =379.844 grad(E)=67.052 E(BOND)=208.227 E(ANGL)=366.208 | | E(DIHE)=0.000 E(IMPR)=94.900 E(VDW )=-256.706 E(ELEC)=-133.616 | | E(CDIH)=3.026 E(NOE )=74.605 E(PLAN)=23.201 | ------------------------------------------------------------------------------- NBONDS: found 66090 intra-atom interactions NBONDS: found 66177 intra-atom interactions NBONDS: found 66267 intra-atom interactions NBONDS: found 66330 intra-atom interactions NBONDS: found 66363 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66396 intra-atom interactions --------------- step= 28750 at 14.37500 ps -------------------------------- | E(kin)+E(total)=1002.188 E(kin)=604.052 temperature=299.333 | | Etotal =398.136 grad(E)=68.411 E(BOND)=226.230 E(ANGL)=365.707 | | E(DIHE)=0.000 E(IMPR)=100.322 E(VDW )=-254.039 E(ELEC)=-135.038 | | E(CDIH)=5.301 E(NOE )=72.871 E(PLAN)=16.783 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66428 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66396 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66365 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 66315 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66274 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66263 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66269 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66189 intra-atom interactions --------------- step= 29000 at 14.50000 ps -------------------------------- | E(kin)+E(total)=991.507 E(kin)=610.027 temperature=302.294 | | Etotal =381.480 grad(E)=65.257 E(BOND)=215.503 E(ANGL)=360.498 | | E(DIHE)=0.000 E(IMPR)=96.863 E(VDW )=-252.352 E(ELEC)=-130.310 | | E(CDIH)=3.061 E(NOE )=66.990 E(PLAN)=21.227 | ------------------------------------------------------------------------------- NBONDS: found 66188 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66140 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 66095 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65981 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65883 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 65827 intra-atom interactions NBONDS: found 65732 intra-atom interactions --------------- step= 29250 at 14.62500 ps -------------------------------- | E(kin)+E(total)=1002.898 E(kin)=610.490 temperature=302.523 | | Etotal =392.409 grad(E)=69.386 E(BOND)=227.937 E(ANGL)=342.566 | | E(DIHE)=0.000 E(IMPR)=95.321 E(VDW )=-252.131 E(ELEC)=-122.464 | | E(CDIH)=5.145 E(NOE )=75.423 E(PLAN)=20.612 | ------------------------------------------------------------------------------- NBONDS: found 65750 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65714 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65728 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65720 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65738 intra-atom interactions NBONDS: found 65757 intra-atom interactions NBONDS: found 65700 intra-atom interactions --------------- step= 29500 at 14.75000 ps -------------------------------- | E(kin)+E(total)=1008.874 E(kin)=623.592 temperature=309.016 | | Etotal =385.282 grad(E)=64.729 E(BOND)=204.805 E(ANGL)=369.888 | | E(DIHE)=0.000 E(IMPR)=95.719 E(VDW )=-269.860 E(ELEC)=-127.211 | | E(CDIH)=2.456 E(NOE )=84.026 E(PLAN)=25.458 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65639 intra-atom interactions NBONDS: found 65650 intra-atom interactions NBONDS: found 65542 intra-atom interactions NBONDS: found 65541 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65432 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65347 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65325 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65353 intra-atom interactions --------------- step= 29750 at 14.87500 ps -------------------------------- | E(kin)+E(total)=1012.208 E(kin)=604.656 temperature=299.633 | | Etotal =407.552 grad(E)=67.084 E(BOND)=230.263 E(ANGL)=348.419 | | E(DIHE)=0.000 E(IMPR)=105.338 E(VDW )=-248.470 E(ELEC)=-116.745 | | E(CDIH)=2.355 E(NOE )=65.423 E(PLAN)=20.968 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65346 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65383 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65473 intra-atom interactions NBONDS: found 65542 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65534 intra-atom interactions NBONDS: found 65578 intra-atom interactions --------------- step= 30000 at 15.00000 ps -------------------------------- | E(kin)+E(total)=989.795 E(kin)=589.252 temperature=291.999 | | Etotal =400.543 grad(E)=68.214 E(BOND)=215.053 E(ANGL)=396.301 | | E(DIHE)=0.000 E(IMPR)=97.438 E(VDW )=-263.105 E(ELEC)=-132.707 | | E(CDIH)=2.310 E(NOE )=66.221 E(PLAN)=19.033 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=997.407 E(kin)=605.478 temperature=300.040 | | Etotal =391.928 grad(E)=67.431 E(BOND)=217.770 E(ANGL)=365.967 | | E(DIHE)=0.000 E(IMPR)=99.118 E(VDW )=-253.795 E(ELEC)=-129.660 | | E(CDIH)=3.326 E(NOE )=70.201 E(PLAN)=19.001 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=9.566 E(kin)=12.896 temperature=6.390 | | Etotal =15.559 grad(E)=1.364 E(BOND)=10.210 E(ANGL)=12.652 | | E(DIHE)=0.000 E(IMPR)=6.534 E(VDW )=6.261 E(ELEC)=6.338 | | E(CDIH)=1.636 E(NOE )=6.086 E(PLAN)=2.595 | ------------------------------------------------------------------------------- --------------- averages for last 30000 steps ----------------------------- | E(kin)+E(total)=995.689 E(kin)=605.287 temperature=299.945 | | Etotal =390.403 grad(E)=66.477 E(BOND)=212.949 E(ANGL)=368.434 | | E(DIHE)=0.000 E(IMPR)=94.906 E(VDW )=-250.860 E(ELEC)=-130.745 | | E(CDIH)=3.684 E(NOE )=72.901 E(PLAN)=19.132 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30000 steps ----------------------- | E(kin)+E(total)=15.837 E(kin)=13.648 temperature=6.763 | | Etotal =17.310 grad(E)=1.746 E(BOND)=11.416 E(ANGL)=13.077 | | E(DIHE)=0.000 E(IMPR)=6.862 E(VDW )=7.450 E(ELEC)=6.669 | | E(CDIH)=1.844 E(NOE )=7.563 E(PLAN)=2.579 | ------------------------------------------------------------------------------- NBONDS: found 65638 intra-atom interactions NBONDS: found 65687 intra-atom interactions NBONDS: found 65723 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65724 intra-atom interactions NBONDS: found 65786 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65739 intra-atom interactions NBONDS: found 65670 intra-atom interactions --------------- step= 30250 at 15.12500 ps -------------------------------- | E(kin)+E(total)=989.169 E(kin)=618.768 temperature=306.625 | | Etotal =370.401 grad(E)=66.291 E(BOND)=214.487 E(ANGL)=358.178 | | E(DIHE)=0.000 E(IMPR)=85.819 E(VDW )=-250.285 E(ELEC)=-137.805 | | E(CDIH)=2.028 E(NOE )=76.078 E(PLAN)=21.901 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65667 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 65658 intra-atom interactions NBONDS: found 65818 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65917 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65993 intra-atom interactions NBONDS: found 66077 intra-atom interactions --------------- step= 30500 at 15.25000 ps -------------------------------- | E(kin)+E(total)=1007.603 E(kin)=612.966 temperature=303.750 | | Etotal =394.637 grad(E)=68.208 E(BOND)=211.100 E(ANGL)=378.325 | | E(DIHE)=0.000 E(IMPR)=94.010 E(VDW )=-244.488 E(ELEC)=-137.499 | | E(CDIH)=1.423 E(NOE )=68.263 E(PLAN)=23.503 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66202 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66217 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66139 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66090 intra-atom interactions NBONDS: found 66009 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65953 intra-atom interactions NBONDS: found 65888 intra-atom interactions --------------- step= 30750 at 15.37500 ps -------------------------------- | E(kin)+E(total)=986.732 E(kin)=591.316 temperature=293.022 | | Etotal =395.416 grad(E)=66.998 E(BOND)=219.039 E(ANGL)=365.281 | | E(DIHE)=0.000 E(IMPR)=97.628 E(VDW )=-258.726 E(ELEC)=-127.790 | | E(CDIH)=8.220 E(NOE )=74.468 E(PLAN)=17.298 | ------------------------------------------------------------------------------- NBONDS: found 65896 intra-atom interactions NBONDS: found 65851 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65741 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65707 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.50 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65714 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65758 intra-atom interactions --------------- step= 31000 at 15.50000 ps -------------------------------- | E(kin)+E(total)=992.153 E(kin)=614.871 temperature=304.694 | | Etotal =377.282 grad(E)=68.057 E(BOND)=229.242 E(ANGL)=356.800 | | E(DIHE)=0.000 E(IMPR)=88.008 E(VDW )=-251.082 E(ELEC)=-121.735 | | E(CDIH)=2.382 E(NOE )=58.130 E(PLAN)=15.537 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart NBONDS: found 65782 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65838 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65891 intra-atom interactions NBONDS: found 65906 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65872 intra-atom interactions NBONDS: found 65858 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65874 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65862 intra-atom interactions --------------- step= 31250 at 15.62500 ps -------------------------------- | E(kin)+E(total)=1004.450 E(kin)=593.042 temperature=293.877 | | Etotal =411.408 grad(E)=70.105 E(BOND)=211.606 E(ANGL)=390.945 | | E(DIHE)=0.000 E(IMPR)=106.072 E(VDW )=-264.400 E(ELEC)=-132.146 | | E(CDIH)=3.481 E(NOE )=77.319 E(PLAN)=18.530 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65869 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65893 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65914 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65919 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65955 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65960 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65969 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 65921 intra-atom interactions --------------- step= 31500 at 15.75000 ps -------------------------------- | E(kin)+E(total)=1001.002 E(kin)=602.847 temperature=298.736 | | Etotal =398.156 grad(E)=65.699 E(BOND)=216.163 E(ANGL)=375.379 | | E(DIHE)=0.000 E(IMPR)=99.742 E(VDW )=-243.030 E(ELEC)=-130.601 | | E(CDIH)=0.968 E(NOE )=61.929 E(PLAN)=17.606 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65897 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65976 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66026 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66062 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66132 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66148 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66171 intra-atom interactions NBONDS: found 66167 intra-atom interactions NBONDS: found 66086 intra-atom interactions --------------- step= 31750 at 15.87500 ps -------------------------------- | E(kin)+E(total)=994.385 E(kin)=593.372 temperature=294.041 | | Etotal =401.013 grad(E)=69.193 E(BOND)=222.869 E(ANGL)=358.273 | | E(DIHE)=0.000 E(IMPR)=114.878 E(VDW )=-255.674 E(ELEC)=-131.834 | | E(CDIH)=1.927 E(NOE )=72.930 E(PLAN)=17.643 | ------------------------------------------------------------------------------- NBONDS: found 66039 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.48 A apart NBONDS: found 65962 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65911 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 65951 intra-atom interactions NBONDS: found 65923 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 65917 intra-atom interactions --------------- step= 32000 at 16.00000 ps -------------------------------- | E(kin)+E(total)=994.857 E(kin)=617.052 temperature=305.775 | | Etotal =377.805 grad(E)=70.223 E(BOND)=206.370 E(ANGL)=355.727 | | E(DIHE)=0.000 E(IMPR)=103.112 E(VDW )=-257.663 E(ELEC)=-128.534 | | E(CDIH)=4.193 E(NOE )=76.671 E(PLAN)=17.928 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65908 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66021 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65991 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66020 intra-atom interactions NBONDS: found 66078 intra-atom interactions NBONDS: found 66101 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66100 intra-atom interactions --------------- step= 32250 at 16.12500 ps -------------------------------- | E(kin)+E(total)=998.075 E(kin)=575.819 temperature=285.342 | | Etotal =422.257 grad(E)=70.562 E(BOND)=212.652 E(ANGL)=404.333 | | E(DIHE)=0.000 E(IMPR)=100.038 E(VDW )=-251.022 E(ELEC)=-132.572 | | E(CDIH)=2.842 E(NOE )=64.761 E(PLAN)=21.225 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart NBONDS: found 66100 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66078 intra-atom interactions NBONDS: found 66093 intra-atom interactions NBONDS: found 66163 intra-atom interactions NBONDS: found 66141 intra-atom interactions NBONDS: found 66174 intra-atom interactions NBONDS: found 66195 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.42 A apart NBONDS: found 66240 intra-atom interactions --------------- step= 32500 at 16.25000 ps -------------------------------- | E(kin)+E(total)=999.008 E(kin)=575.757 temperature=285.312 | | Etotal =423.251 grad(E)=69.404 E(BOND)=233.586 E(ANGL)=392.656 | | E(DIHE)=0.000 E(IMPR)=88.484 E(VDW )=-255.764 E(ELEC)=-134.104 | | E(CDIH)=4.087 E(NOE )=76.012 E(PLAN)=18.295 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=997.779 E(kin)=605.433 temperature=300.017 | | Etotal =392.347 grad(E)=68.251 E(BOND)=217.355 E(ANGL)=369.434 | | E(DIHE)=0.000 E(IMPR)=97.466 E(VDW )=-253.379 E(ELEC)=-130.740 | | E(CDIH)=3.330 E(NOE )=69.653 E(PLAN)=19.227 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=8.603 E(kin)=12.296 temperature=6.093 | | Etotal =14.494 grad(E)=1.468 E(BOND)=9.330 E(ANGL)=12.420 | | E(DIHE)=0.000 E(IMPR)=6.639 E(VDW )=6.879 E(ELEC)=4.453 | | E(CDIH)=1.819 E(NOE )=6.945 E(PLAN)=2.309 | ------------------------------------------------------------------------------- --------------- averages for last 32500 steps ----------------------------- | E(kin)+E(total)=995.850 E(kin)=605.298 temperature=299.951 | | Etotal =390.552 grad(E)=66.613 E(BOND)=213.288 E(ANGL)=368.511 | | E(DIHE)=0.000 E(IMPR)=95.103 E(VDW )=-251.053 E(ELEC)=-130.745 | | E(CDIH)=3.657 E(NOE )=72.651 E(PLAN)=19.139 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 32500 steps ----------------------- | E(kin)+E(total)=15.411 E(kin)=13.549 temperature=6.714 | | Etotal =17.118 grad(E)=1.790 E(BOND)=11.330 E(ANGL)=13.030 | | E(DIHE)=0.000 E(IMPR)=6.879 E(VDW )=7.438 E(ELEC)=6.525 | | E(CDIH)=1.844 E(NOE )=7.567 E(PLAN)=2.560 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66255 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.50 A apart NBONDS: found 66209 intra-atom interactions NBONDS: found 66160 intra-atom interactions NBONDS: found 66126 intra-atom interactions NBONDS: found 65996 intra-atom interactions NBONDS: found 65972 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65871 intra-atom interactions --------------- step= 32750 at 16.37500 ps -------------------------------- | E(kin)+E(total)=1000.139 E(kin)=599.541 temperature=297.098 | | Etotal =400.598 grad(E)=68.003 E(BOND)=240.651 E(ANGL)=371.589 | | E(DIHE)=0.000 E(IMPR)=85.451 E(VDW )=-250.594 E(ELEC)=-131.541 | | E(CDIH)=3.048 E(NOE )=61.525 E(PLAN)=20.468 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65793 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65746 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 65689 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65716 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65635 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.44 A apart NBONDS: found 65691 intra-atom interactions --------------- step= 33000 at 16.50000 ps -------------------------------- | E(kin)+E(total)=1001.701 E(kin)=595.176 temperature=294.935 | | Etotal =406.525 grad(E)=69.572 E(BOND)=222.121 E(ANGL)=381.258 | | E(DIHE)=0.000 E(IMPR)=93.891 E(VDW )=-244.629 E(ELEC)=-134.968 | | E(CDIH)=2.657 E(NOE )=64.707 E(PLAN)=21.488 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65702 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65673 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65630 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65553 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65511 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65534 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65577 intra-atom interactions --------------- step= 33250 at 16.62500 ps -------------------------------- | E(kin)+E(total)=1003.402 E(kin)=603.792 temperature=299.204 | | Etotal =399.610 grad(E)=68.715 E(BOND)=239.459 E(ANGL)=361.417 | | E(DIHE)=0.000 E(IMPR)=90.622 E(VDW )=-254.665 E(ELEC)=-128.230 | | E(CDIH)=1.194 E(NOE )=74.194 E(PLAN)=15.617 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65704 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65807 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65897 intra-atom interactions NBONDS: found 65900 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65915 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65922 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65869 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65832 intra-atom interactions --------------- step= 33500 at 16.75000 ps -------------------------------- | E(kin)+E(total)=988.445 E(kin)=601.410 temperature=298.024 | | Etotal =387.036 grad(E)=70.244 E(BOND)=211.072 E(ANGL)=381.297 | | E(DIHE)=0.000 E(IMPR)=94.276 E(VDW )=-264.009 E(ELEC)=-131.930 | | E(CDIH)=2.560 E(NOE )=75.075 E(PLAN)=18.695 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65839 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65830 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65860 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65933 intra-atom interactions NBONDS: found 66002 intra-atom interactions NBONDS: found 66031 intra-atom interactions --------------- step= 33750 at 16.87500 ps -------------------------------- | E(kin)+E(total)=996.521 E(kin)=615.054 temperature=304.785 | | Etotal =381.467 grad(E)=67.267 E(BOND)=205.951 E(ANGL)=375.495 | | E(DIHE)=0.000 E(IMPR)=80.059 E(VDW )=-240.058 E(ELEC)=-138.562 | | E(CDIH)=3.151 E(NOE )=76.360 E(PLAN)=19.070 | ------------------------------------------------------------------------------- NBONDS: found 65988 intra-atom interactions NBONDS: found 65909 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65898 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.43 A apart NBONDS: found 65841 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65802 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65738 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65741 intra-atom interactions --------------- step= 34000 at 17.00000 ps -------------------------------- | E(kin)+E(total)=1001.869 E(kin)=594.980 temperature=294.838 | | Etotal =406.889 grad(E)=70.399 E(BOND)=233.381 E(ANGL)=371.146 | | E(DIHE)=0.000 E(IMPR)=93.080 E(VDW )=-245.264 E(ELEC)=-135.266 | | E(CDIH)=5.068 E(NOE )=64.723 E(PLAN)=20.022 | ------------------------------------------------------------------------------- NBONDS: found 65713 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65745 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65753 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65798 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.38 A apart NBONDS: found 65773 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 65832 intra-atom interactions --------------- step= 34250 at 17.12500 ps -------------------------------- | E(kin)+E(total)=1003.834 E(kin)=604.991 temperature=299.798 | | Etotal =398.843 grad(E)=68.597 E(BOND)=213.520 E(ANGL)=368.492 | | E(DIHE)=0.000 E(IMPR)=100.621 E(VDW )=-251.677 E(ELEC)=-133.975 | | E(CDIH)=5.607 E(NOE )=76.931 E(PLAN)=19.325 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65834 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65804 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65796 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart NBONDS: found 65776 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65689 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65656 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65599 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65591 intra-atom interactions --------------- step= 34500 at 17.25000 ps -------------------------------- | E(kin)+E(total)=1006.238 E(kin)=600.105 temperature=297.377 | | Etotal =406.133 grad(E)=69.936 E(BOND)=224.008 E(ANGL)=389.529 | | E(DIHE)=0.000 E(IMPR)=87.349 E(VDW )=-255.952 E(ELEC)=-130.956 | | E(CDIH)=1.386 E(NOE )=71.493 E(PLAN)=19.277 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65627 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 65688 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65657 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.50 A apart NBONDS: found 65656 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.46 A apart NBONDS: found 65616 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65591 intra-atom interactions --------------- step= 34750 at 17.37500 ps -------------------------------- | E(kin)+E(total)=998.858 E(kin)=599.174 temperature=296.916 | | Etotal =399.684 grad(E)=71.310 E(BOND)=237.519 E(ANGL)=353.249 | | E(DIHE)=0.000 E(IMPR)=92.777 E(VDW )=-250.728 E(ELEC)=-138.113 | | E(CDIH)=6.444 E(NOE )=83.529 E(PLAN)=15.008 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65552 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart NBONDS: found 65488 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65414 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65436 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65420 intra-atom interactions %atoms "A -9 -URI -O2' " and "A -10 -CYT -H3' " only 1.50 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65394 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65413 intra-atom interactions NBONDS: found 65462 intra-atom interactions --------------- step= 35000 at 17.50000 ps -------------------------------- | E(kin)+E(total)=1019.079 E(kin)=625.392 temperature=309.908 | | Etotal =393.687 grad(E)=68.576 E(BOND)=210.259 E(ANGL)=371.003 | | E(DIHE)=0.000 E(IMPR)=106.882 E(VDW )=-241.539 E(ELEC)=-135.878 | | E(CDIH)=2.288 E(NOE )=61.835 E(PLAN)=18.838 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=997.298 E(kin)=605.416 temperature=300.009 | | Etotal =391.882 grad(E)=68.748 E(BOND)=220.206 E(ANGL)=368.449 | | E(DIHE)=0.000 E(IMPR)=96.190 E(VDW )=-251.735 E(ELEC)=-133.378 | | E(CDIH)=3.445 E(NOE )=69.831 E(PLAN)=18.873 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.567 E(kin)=12.479 temperature=6.184 | | Etotal =14.167 grad(E)=1.428 E(BOND)=10.177 E(ANGL)=11.377 | | E(DIHE)=0.000 E(IMPR)=6.382 E(VDW )=6.225 E(ELEC)=4.088 | | E(CDIH)=1.644 E(NOE )=6.268 E(PLAN)=1.778 | ------------------------------------------------------------------------------- --------------- averages for last 35000 steps ----------------------------- | E(kin)+E(total)=995.954 E(kin)=605.306 temperature=299.955 | | Etotal =390.647 grad(E)=66.766 E(BOND)=213.782 E(ANGL)=368.507 | | E(DIHE)=0.000 E(IMPR)=95.181 E(VDW )=-251.102 E(ELEC)=-130.933 | | E(CDIH)=3.642 E(NOE )=72.450 E(PLAN)=19.120 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 35000 steps ----------------------- | E(kin)+E(total)=14.992 E(kin)=13.475 temperature=6.677 | | Etotal =16.928 grad(E)=1.850 E(BOND)=11.392 E(ANGL)=12.919 | | E(DIHE)=0.000 E(IMPR)=6.851 E(VDW )=7.360 E(ELEC)=6.418 | | E(CDIH)=1.832 E(NOE )=7.517 E(PLAN)=2.513 | ------------------------------------------------------------------------------- NBONDS: found 65463 intra-atom interactions NBONDS: found 65448 intra-atom interactions NBONDS: found 65456 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65470 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65445 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65502 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65522 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 65519 intra-atom interactions --------------- step= 35250 at 17.62500 ps -------------------------------- | E(kin)+E(total)=994.511 E(kin)=596.937 temperature=295.808 | | Etotal =397.574 grad(E)=69.598 E(BOND)=213.265 E(ANGL)=387.216 | | E(DIHE)=0.000 E(IMPR)=99.891 E(VDW )=-249.113 E(ELEC)=-142.991 | | E(CDIH)=4.296 E(NOE )=70.421 E(PLAN)=14.589 | ------------------------------------------------------------------------------- %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.48 A apart NBONDS: found 65494 intra-atom interactions NBONDS: found 65503 intra-atom interactions NBONDS: found 65457 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65398 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65389 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65373 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65399 intra-atom interactions NBONDS: found 65439 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65499 intra-atom interactions --------------- step= 35500 at 17.75000 ps -------------------------------- | E(kin)+E(total)=1005.503 E(kin)=620.065 temperature=307.268 | | Etotal =385.439 grad(E)=69.810 E(BOND)=217.724 E(ANGL)=366.154 | | E(DIHE)=0.000 E(IMPR)=97.149 E(VDW )=-246.931 E(ELEC)=-140.494 | | E(CDIH)=6.228 E(NOE )=66.309 E(PLAN)=19.300 | ------------------------------------------------------------------------------- NBONDS: found 65544 intra-atom interactions NBONDS: found 65542 intra-atom interactions NBONDS: found 65620 intra-atom interactions NBONDS: found 65647 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65734 intra-atom interactions --------------- step= 35750 at 17.87500 ps -------------------------------- | E(kin)+E(total)=997.355 E(kin)=613.090 temperature=303.812 | | Etotal =384.265 grad(E)=70.399 E(BOND)=218.651 E(ANGL)=372.350 | | E(DIHE)=0.000 E(IMPR)=97.801 E(VDW )=-266.406 E(ELEC)=-130.247 | | E(CDIH)=6.677 E(NOE )=67.547 E(PLAN)=17.891 | ------------------------------------------------------------------------------- NBONDS: found 65845 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65916 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65969 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65983 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65956 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.44 A apart NBONDS: found 65978 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.42 A apart NBONDS: found 65872 intra-atom interactions --------------- step= 36000 at 18.00000 ps -------------------------------- | E(kin)+E(total)=989.203 E(kin)=616.861 temperature=305.680 | | Etotal =372.342 grad(E)=68.219 E(BOND)=204.069 E(ANGL)=373.062 | | E(DIHE)=0.000 E(IMPR)=90.006 E(VDW )=-250.984 E(ELEC)=-128.319 | | E(CDIH)=2.844 E(NOE )=63.371 E(PLAN)=18.292 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 65853 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 65800 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65786 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65791 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65816 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65852 intra-atom interactions --------------- step= 36250 at 18.12500 ps -------------------------------- | E(kin)+E(total)=1002.443 E(kin)=600.169 temperature=297.409 | | Etotal =402.274 grad(E)=69.219 E(BOND)=227.312 E(ANGL)=369.358 | | E(DIHE)=0.000 E(IMPR)=103.496 E(VDW )=-264.219 E(ELEC)=-129.087 | | E(CDIH)=4.998 E(NOE )=69.256 E(PLAN)=21.160 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65955 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart NBONDS: found 66036 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 66133 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66171 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.45 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66173 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66137 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66138 intra-atom interactions --------------- step= 36500 at 18.25000 ps -------------------------------- | E(kin)+E(total)=988.647 E(kin)=594.386 temperature=294.543 | | Etotal =394.261 grad(E)=69.623 E(BOND)=232.607 E(ANGL)=356.314 | | E(DIHE)=0.000 E(IMPR)=100.611 E(VDW )=-247.275 E(ELEC)=-135.458 | | E(CDIH)=3.784 E(NOE )=60.154 E(PLAN)=23.525 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 66090 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66070 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66043 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66038 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 66043 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66102 intra-atom interactions NBONDS: found 66084 intra-atom interactions NBONDS: found 66116 intra-atom interactions NBONDS: found 66173 intra-atom interactions --------------- step= 36750 at 18.37500 ps -------------------------------- | E(kin)+E(total)=1009.486 E(kin)=602.662 temperature=298.645 | | Etotal =406.824 grad(E)=69.290 E(BOND)=235.617 E(ANGL)=363.649 | | E(DIHE)=0.000 E(IMPR)=97.479 E(VDW )=-254.894 E(ELEC)=-136.951 | | E(CDIH)=4.330 E(NOE )=80.249 E(PLAN)=17.345 | ------------------------------------------------------------------------------- NBONDS: found 66211 intra-atom interactions NBONDS: found 66238 intra-atom interactions NBONDS: found 66203 intra-atom interactions NBONDS: found 66246 intra-atom interactions NBONDS: found 66228 intra-atom interactions NBONDS: found 66201 intra-atom interactions NBONDS: found 66230 intra-atom interactions NBONDS: found 66216 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 66184 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66199 intra-atom interactions NBONDS: found 66260 intra-atom interactions --------------- step= 37000 at 18.50000 ps -------------------------------- | E(kin)+E(total)=1001.253 E(kin)=624.983 temperature=309.705 | | Etotal =376.270 grad(E)=65.730 E(BOND)=190.766 E(ANGL)=375.177 | | E(DIHE)=0.000 E(IMPR)=104.188 E(VDW )=-246.407 E(ELEC)=-135.015 | | E(CDIH)=3.515 E(NOE )=67.635 E(PLAN)=16.409 | ------------------------------------------------------------------------------- NBONDS: found 66319 intra-atom interactions NBONDS: found 66394 intra-atom interactions NBONDS: found 66345 intra-atom interactions NBONDS: found 66362 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.48 A apart NBONDS: found 66334 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 66359 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66381 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66381 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66386 intra-atom interactions --------------- step= 37250 at 18.62500 ps -------------------------------- | E(kin)+E(total)=1000.299 E(kin)=582.876 temperature=288.839 | | Etotal =417.423 grad(E)=70.853 E(BOND)=225.565 E(ANGL)=378.740 | | E(DIHE)=0.000 E(IMPR)=107.963 E(VDW )=-245.672 E(ELEC)=-137.001 | | E(CDIH)=2.853 E(NOE )=69.029 E(PLAN)=15.946 | ------------------------------------------------------------------------------- NBONDS: found 66325 intra-atom interactions NBONDS: found 66263 intra-atom interactions NBONDS: found 66187 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 66128 intra-atom interactions NBONDS: found 66049 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.41 A apart NBONDS: found 65912 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart NBONDS: found 65931 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65936 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65961 intra-atom interactions --------------- step= 37500 at 18.75000 ps -------------------------------- | E(kin)+E(total)=999.574 E(kin)=615.487 temperature=304.999 | | Etotal =384.087 grad(E)=66.458 E(BOND)=223.937 E(ANGL)=356.739 | | E(DIHE)=0.000 E(IMPR)=97.324 E(VDW )=-257.940 E(ELEC)=-133.416 | | E(CDIH)=4.660 E(NOE )=73.049 E(PLAN)=19.735 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=998.236 E(kin)=605.572 temperature=300.086 | | Etotal =392.664 grad(E)=69.606 E(BOND)=222.328 E(ANGL)=368.889 | | E(DIHE)=0.000 E(IMPR)=96.869 E(VDW )=-251.542 E(ELEC)=-135.207 | | E(CDIH)=3.169 E(NOE )=69.399 E(PLAN)=18.759 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=7.193 E(kin)=12.919 temperature=6.402 | | Etotal =14.264 grad(E)=1.564 E(BOND)=10.075 E(ANGL)=12.043 | | E(DIHE)=0.000 E(IMPR)=7.367 E(VDW )=6.753 E(ELEC)=4.192 | | E(CDIH)=1.658 E(NOE )=6.311 E(PLAN)=2.134 | ------------------------------------------------------------------------------- --------------- averages for last 37500 steps ----------------------------- | E(kin)+E(total)=996.106 E(kin)=605.324 temperature=299.964 | | Etotal =390.782 grad(E)=66.955 E(BOND)=214.352 E(ANGL)=368.532 | | E(DIHE)=0.000 E(IMPR)=95.293 E(VDW )=-251.131 E(ELEC)=-131.218 | | E(CDIH)=3.610 E(NOE )=72.247 E(PLAN)=19.096 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 37500 steps ----------------------- | E(kin)+E(total)=14.614 E(kin)=13.439 temperature=6.660 | | Etotal =16.771 grad(E)=1.964 E(BOND)=11.508 E(ANGL)=12.863 | | E(DIHE)=0.000 E(IMPR)=6.899 E(VDW )=7.322 E(ELEC)=6.384 | | E(CDIH)=1.824 E(NOE )=7.481 E(PLAN)=2.491 | ------------------------------------------------------------------------------- NBONDS: found 65953 intra-atom interactions NBONDS: found 65909 intra-atom interactions NBONDS: found 65893 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart NBONDS: found 65980 intra-atom interactions %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 65996 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 66015 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 65999 intra-atom interactions --------------- step= 37750 at 18.87500 ps -------------------------------- | E(kin)+E(total)=997.019 E(kin)=604.896 temperature=299.752 | | Etotal =392.123 grad(E)=70.672 E(BOND)=204.816 E(ANGL)=367.798 | | E(DIHE)=0.000 E(IMPR)=108.689 E(VDW )=-252.416 E(ELEC)=-133.672 | | E(CDIH)=3.876 E(NOE )=72.361 E(PLAN)=20.670 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65974 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.47 A apart NBONDS: found 65943 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.46 A apart NBONDS: found 65949 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65910 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart NBONDS: found 65887 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65852 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 65834 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.36 A apart NBONDS: found 65829 intra-atom interactions --------------- step= 38000 at 19.00000 ps -------------------------------- | E(kin)+E(total)=1004.678 E(kin)=613.257 temperature=303.894 | | Etotal =391.422 grad(E)=68.491 E(BOND)=232.601 E(ANGL)=344.994 | | E(DIHE)=0.000 E(IMPR)=88.903 E(VDW )=-252.223 E(ELEC)=-128.697 | | E(CDIH)=3.147 E(NOE )=83.062 E(PLAN)=19.636 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65812 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65846 intra-atom interactions NBONDS: found 65956 intra-atom interactions NBONDS: found 65997 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.50 A apart NBONDS: found 66062 intra-atom interactions NBONDS: found 66058 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 66100 intra-atom interactions --------------- step= 38250 at 19.12500 ps -------------------------------- | E(kin)+E(total)=989.912 E(kin)=606.330 temperature=300.462 | | Etotal =383.582 grad(E)=67.968 E(BOND)=218.454 E(ANGL)=363.052 | | E(DIHE)=0.000 E(IMPR)=94.866 E(VDW )=-244.497 E(ELEC)=-135.368 | | E(CDIH)=3.755 E(NOE )=62.911 E(PLAN)=20.409 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 66038 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 66021 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66031 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66022 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.41 A apart NBONDS: found 66055 intra-atom interactions NBONDS: found 66053 intra-atom interactions NBONDS: found 65992 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66021 intra-atom interactions --------------- step= 38500 at 19.25000 ps -------------------------------- | E(kin)+E(total)=1002.047 E(kin)=610.785 temperature=302.670 | | Etotal =391.262 grad(E)=67.684 E(BOND)=209.350 E(ANGL)=366.745 | | E(DIHE)=0.000 E(IMPR)=95.681 E(VDW )=-255.210 E(ELEC)=-133.299 | | E(CDIH)=4.500 E(NOE )=82.101 E(PLAN)=21.393 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66066 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.39 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66099 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.35 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.40 A apart NBONDS: found 66107 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66042 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.38 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66075 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.42 A apart NBONDS: found 66133 intra-atom interactions %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 66240 intra-atom interactions --------------- step= 38750 at 19.37500 ps -------------------------------- | E(kin)+E(total)=1008.746 E(kin)=577.430 temperature=286.141 | | Etotal =431.315 grad(E)=71.190 E(BOND)=231.646 E(ANGL)=388.157 | | E(DIHE)=0.000 E(IMPR)=102.958 E(VDW )=-243.238 E(ELEC)=-136.716 | | E(CDIH)=5.801 E(NOE )=62.545 E(PLAN)=20.163 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.41 A apart NBONDS: found 66322 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.41 A apart NBONDS: found 66370 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 66397 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.44 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.45 A apart NBONDS: found 66374 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66338 intra-atom interactions NBONDS: found 66337 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 66266 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 66200 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.47 A apart NBONDS: found 66118 intra-atom interactions --------------- step= 39000 at 19.50000 ps -------------------------------- | E(kin)+E(total)=994.205 E(kin)=595.188 temperature=294.941 | | Etotal =399.017 grad(E)=68.936 E(BOND)=213.901 E(ANGL)=375.641 | | E(DIHE)=0.000 E(IMPR)=107.383 E(VDW )=-261.750 E(ELEC)=-129.066 | | E(CDIH)=2.011 E(NOE )=70.605 E(PLAN)=20.293 | ------------------------------------------------------------------------------- %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 66028 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65914 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.41 A apart NBONDS: found 65874 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.44 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.46 A apart NBONDS: found 65865 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.49 A apart NBONDS: found 65772 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65722 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.45 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart %atoms "A -13 -ADE -O5' " and "A -13 -ADE -H8 " only 1.49 A apart NBONDS: found 65722 intra-atom interactions --------------- step= 39250 at 19.62500 ps -------------------------------- | E(kin)+E(total)=1000.661 E(kin)=597.887 temperature=296.278 | | Etotal =402.774 grad(E)=69.836 E(BOND)=223.042 E(ANGL)=368.379 | | E(DIHE)=0.000 E(IMPR)=92.277 E(VDW )=-243.833 E(ELEC)=-125.178 | | E(CDIH)=1.398 E(NOE )=65.685 E(PLAN)=21.006 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart NBONDS: found 65737 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.47 A apart NBONDS: found 65701 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.46 A apart %atoms "A -14 -ADE -O5' " and "A -14 -ADE -H8 " only 1.49 A apart NBONDS: found 65690 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.47 A apart NBONDS: found 65678 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 65649 intra-atom interactions %atoms "A -10 -CYT -O5' " and "A -10 -CYT -H6 " only 1.49 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65671 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65665 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.45 A apart NBONDS: found 65723 intra-atom interactions %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.46 A apart NBONDS: found 65722 intra-atom interactions --------------- step= 39500 at 19.75000 ps -------------------------------- | E(kin)+E(total)=995.924 E(kin)=581.807 temperature=288.310 | | Etotal =414.117 grad(E)=68.497 E(BOND)=230.528 E(ANGL)=384.573 | | E(DIHE)=0.000 E(IMPR)=99.188 E(VDW )=-261.361 E(ELEC)=-136.034 | | E(CDIH)=1.415 E(NOE )=79.204 E(PLAN)=16.603 | ------------------------------------------------------------------------------- %atoms "A -9 -URI -HO2'" and "A -10 -CYT -H3' " only 1.47 A apart %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.48 A apart NBONDS: found 65759 intra-atom interactions NBONDS: found 65846 intra-atom interactions NBONDS: found 65970 intra-atom interactions NBONDS: found 66004 intra-atom interactions NBONDS: found 66104 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.50 A apart %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.48 A apart NBONDS: found 66074 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.42 A apart NBONDS: found 66122 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.45 A apart NBONDS: found 66165 intra-atom interactions %atoms "A -13 -ADE -H2' " and "A -14 -ADE -O4' " only 1.39 A apart NBONDS: found 66218 intra-atom interactions --------------- step= 39750 at 19.87500 ps -------------------------------- | E(kin)+E(total)=1009.249 E(kin)=604.794 temperature=299.701 | | Etotal =404.455 grad(E)=71.168 E(BOND)=221.166 E(ANGL)=365.432 | | E(DIHE)=0.000 E(IMPR)=107.985 E(VDW )=-250.012 E(ELEC)=-134.636 | | E(CDIH)=3.297 E(NOE )=70.889 E(PLAN)=20.334 | ------------------------------------------------------------------------------- %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66236 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.40 A apart NBONDS: found 66270 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66212 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66175 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.42 A apart NBONDS: found 66212 intra-atom interactions NBONDS: found 66146 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 66071 intra-atom interactions %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.43 A apart NBONDS: found 66027 intra-atom interactions --------------- step= 40000 at 20.00000 ps -------------------------------- | E(kin)+E(total)=999.814 E(kin)=606.960 temperature=300.774 | | Etotal =392.854 grad(E)=69.611 E(BOND)=233.217 E(ANGL)=362.235 | | E(DIHE)=0.000 E(IMPR)=100.262 E(VDW )=-255.215 E(ELEC)=-130.797 | | E(CDIH)=1.221 E(NOE )=62.870 E(PLAN)=19.061 | ------------------------------------------------------------------------------- --------------- averages for last 2500 steps ----------------------------- | E(kin)+E(total)=999.628 E(kin)=605.481 temperature=300.041 | | Etotal =394.147 grad(E)=69.243 E(BOND)=223.624 E(ANGL)=365.504 | | E(DIHE)=0.000 E(IMPR)=98.260 E(VDW )=-253.296 E(ELEC)=-131.444 | | E(CDIH)=3.486 E(NOE )=68.581 E(PLAN)=19.431 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 2500 steps ----------------------- | E(kin)+E(total)=6.836 E(kin)=12.717 temperature=6.302 | | Etotal =13.996 grad(E)=1.413 E(BOND)=10.352 E(ANGL)=12.420 | | E(DIHE)=0.000 E(IMPR)=6.797 E(VDW )=6.869 E(ELEC)=4.730 | | E(CDIH)=1.778 E(NOE )=7.059 E(PLAN)=2.216 | ------------------------------------------------------------------------------- --------------- averages for last 40000 steps ----------------------------- | E(kin)+E(total)=996.326 E(kin)=605.334 temperature=299.968 | | Etotal =390.992 grad(E)=67.098 E(BOND)=214.932 E(ANGL)=368.343 | | E(DIHE)=0.000 E(IMPR)=95.479 E(VDW )=-251.267 E(ELEC)=-131.232 | | E(CDIH)=3.603 E(NOE )=72.018 E(PLAN)=19.117 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40000 steps ----------------------- | E(kin)+E(total)=14.278 E(kin)=13.395 temperature=6.638 | | Etotal =16.631 grad(E)=2.012 E(BOND)=11.657 E(ANGL)=12.856 | | E(DIHE)=0.000 E(IMPR)=6.930 E(VDW )=7.313 E(ELEC)=6.294 | | E(CDIH)=1.822 E(NOE )=7.508 E(PLAN)=2.476 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 0.06896 -0.01173 0.04912 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 09:54:29 created by user: READC: reading file= 1 ISTART= 200 READC: 677 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 20000 SKIP= 200 STOP= 40000 READC: TIMEstep= 0.00050000 ps header= CORD READC: complete. 101 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR>close refine.tra end ! disposition=delete doesn't work X-PLOR> X-PLOR>! Final minimization. X-PLOR> X-PLOR>minimize powell nstep=200 nprint=25 end POWELL: number of degrees of freedom= 2031 %atoms "A -10 -CYT -H2' " and "A -11 -ADE -O4' " only 1.49 A apart NBONDS: found 65947 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0001 ----------------------- | Etotal =-193.955 grad(E)=4.285 E(BOND)=10.976 E(ANGL)=115.018 | | E(DIHE)=0.000 E(IMPR)=18.105 E(VDW )=-265.617 E(ELEC)=-133.486 | | E(CDIH)=1.068 E(NOE )=42.995 E(PLAN)=16.986 | ------------------------------------------------------------------------------- NBONDS: found 65947 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =-210.697 grad(E)=3.429 E(BOND)=8.259 E(ANGL)=104.230 | | E(DIHE)=0.000 E(IMPR)=17.832 E(VDW )=-267.447 E(ELEC)=-134.727 | | E(CDIH)=1.236 E(NOE )=43.998 E(PLAN)=15.922 | ------------------------------------------------------------------------------- --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =-216.747 grad(E)=1.219 E(BOND)=7.826 E(ANGL)=102.029 | | E(DIHE)=0.000 E(IMPR)=16.809 E(VDW )=-266.560 E(ELEC)=-136.812 | | E(CDIH)=1.460 E(NOE )=43.347 E(PLAN)=15.155 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =-218.842 grad(E)=1.314 E(BOND)=7.763 E(ANGL)=102.764 | | E(DIHE)=0.000 E(IMPR)=16.507 E(VDW )=-266.400 E(ELEC)=-138.524 | | E(CDIH)=1.428 E(NOE )=42.750 E(PLAN)=14.871 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =-220.300 grad(E)=1.245 E(BOND)=7.935 E(ANGL)=102.947 | | E(DIHE)=0.000 E(IMPR)=16.402 E(VDW )=-266.489 E(ELEC)=-140.102 | | E(CDIH)=1.399 E(NOE )=42.988 E(PLAN)=14.620 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =-221.453 grad(E)=1.051 E(BOND)=7.903 E(ANGL)=103.393 | | E(DIHE)=0.000 E(IMPR)=16.649 E(VDW )=-266.575 E(ELEC)=-141.767 | | E(CDIH)=1.321 E(NOE )=43.253 E(PLAN)=14.369 | ------------------------------------------------------------------------------- --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =-222.452 grad(E)=1.343 E(BOND)=7.888 E(ANGL)=102.988 | | E(DIHE)=0.000 E(IMPR)=16.933 E(VDW )=-265.458 E(ELEC)=-143.350 | | E(CDIH)=1.265 E(NOE )=42.977 E(PLAN)=14.305 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =-223.051 grad(E)=0.815 E(BOND)=7.840 E(ANGL)=103.102 | | E(DIHE)=0.000 E(IMPR)=16.561 E(VDW )=-264.943 E(ELEC)=-144.214 | | E(CDIH)=1.211 E(NOE )=42.953 E(PLAN)=14.440 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>! Analyze and write out the final structure. X-PLOR> X-PLOR>print threshold=0.05 bonds (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.050: 0 RMS deviation= 0.002 X-PLOR>evaluate ($rms_bond=$result) EVALUATE: symbol $RMS_BOND set to 0.225080E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (A 9 C4' |A 9 C3' |A 9 O3' ) 118.572 110.500 8.072 8.832 445.032 (A 9 O3' |A 10 P |A 10 O2P ) 114.452 108.300 6.152 3.387 293.791 Number of violations greater 5.000: 2 RMS deviation= 0.718 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.717568 (real) X-PLOR>evaluate ($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 $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.438 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.438425 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR>print threshold=0.2 noe ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++ CLASS NIL +++++++++++++++++++++++++++++++++++ for this class: SCALe= 100.000 AVERage=center POTEntial=square-well SQCOnstant= 1.000 SQEXponent= 2 SQOFfset= 0.000 ======================================== set-i-atoms A 11 ADE H8 set-j-atoms A 12 URI H6 R= 5.323 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.323 E(NOE)= 10.449 ======================================== set-i-atoms A 12 URI H4' set-j-atoms A 13 ADE H8 R= 2.773 NOE= 4.00 (- 1.00/+ 1.00) Delta= 0.227 E(NOE)= 5.170 ======================================== set-i-atoms A 12 URI H6 set-j-atoms A 13 ADE H8 R= 5.251 NOE= 4.00 (- 1.00/+ 1.00) Delta= -0.251 E(NOE)= 6.325 NOEPRI: RMS diff. = 0.022, #(violat.> 0.2)= 3 of 928 NOEs NOEPRI: RMS diff. class NIL = 0.022, #(viol.> 0.2)= 3 of 928 NOEs X-PLOR>evaluate ($rms_noe=$result) EVALUATE: symbol $RMS_NOE set to 0.215140E-01 (real) X-PLOR>evaluate ($v_noe=$violations) EVALUATE: symbol $V_NOE set to 3.00000 (real) X-PLOR>print threshold=5 cdih Total number of dihedral angle restraints= 203 overall scale = 800.0000 Number of dihedral angle restraints= 203 Number of violations greater than 5.000: 0 RMS deviation= 0.156 X-PLOR>evaluate ($rms_cdih=$result) EVALUATE: symbol $RMS_CDIH set to 0.156488 (real) X-PLOR>evaluate ($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 7.83963, angle 103.102, dihedral 0, improper 16.5605, NOE 42.9527, c-dihedral 1.21144, planar 14.4401, VdW -264.943, elec -144.214, total -223.051 RMSD: bond 2.250803E-03, angle 0.717568, dihedral 0, improper 0.438425, NOE 2.151401E-02, c-dihedral 0.156488 Violations: bond 0, angle 2, dihedral 0, improper 0, NOE 3, 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= 136143 current use= 0 X-PLOR: total CPU time= 2985.0422 s X-PLOR: entry time at 09:53:58 17-Aug-96 X-PLOR: exit time at 10:44:02 17-Aug-96