X-PLOR: V3.834 user: on: Alpha/OSF at: 27-Apr-96 13:41:23 Author: Axel T. Brunger Copyright: 1988-96 (Yale University), 1987 (Harvard University) X-PLOR>! make-template.inp -- Build extended structure for local geometry reference X-PLOR>! Dave Schweisguth , 27 Apr 1996 X-PLOR>! Derived from nmr/generate_template.inp X-PLOR> X-PLOR>set seed=@xplor.seed end ! Use xplor -s ASSFIL: file /sgi/people/dcs/ws/xplor/italy2.4x/xplor.seed opened. SEED=100399.755981445 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) X-PLOR> X-PLOR>vector ident (x) (all) ! Set X coordinate to atom number(!) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (x=x/10) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (y=random(0.5)) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (z=random(0.5)) (all) SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (fbeta=50) (all) ! Friction coefficient, in 1/ps SELRPN: 677 atoms have been selected out of 677 X-PLOR>vector do (mass=100) (all) ! Heavy masses, in amu SELRPN: 677 atoms have been selected out of 677 X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> cutnb=5.5 NBDSET> rconst=20 NBDSET> nbxmod=-2 NBDSET> repel=0.9 ! Repulsive non-bonded energy only NBDSET> wmin=0.1 NBDSET> tolerance=1 NBDSET> rexp=2 ! default NBDSET> irexp=2 ! default NBDSET> inhibit=0.25 NBDSET> end PARRDR>end X-PLOR> X-PLOR>! Parameter set may or may not contain dihedral energies X-PLOR> X-PLOR>flags exclude * include bond angle dihe vdw end X-PLOR>minimize powell nstep=200 nprint=10 end POWELL: number of degrees of freedom= 2031 CODBON: bond type-based parameters retrieved CODANG: angle type-based parameters retrieved NBUPDA: type-based van der Waals parameters retrieved. NBONDS: generating intra-molecular exclusion list with mode=-2 MAKINB: mode -2 found 728 exclusions and 0 interactions(1-4) NBONDS: found 34336 intra-atom interactions NBONDS: found 32949 intra-atom interactions NBONDS: found 28946 intra-atom interactions %atoms "A -3 -CYT -C4' " and "A -3 -CYT -N3 " only 0.08 A apart %atoms "A -15 -CYT -O3' " and "A -16 -CYT -O5' " only 0.04 A apart NBONDS: found 29609 intra-atom interactions --------------- cycle= 10 ------ stepsize= 0.0000 ----------------------- | Etotal =0.45E+07 grad(E)=2766.828 E(BOND)=0.12E+07 E(ANGL)=640941.226 | | E(DIHE)=0.000 E(VDW )=0.27E+07 | ------------------------------------------------------------------------------- NBONDS: found 28460 intra-atom interactions NBONDS: found 25478 intra-atom interactions %atoms "A -4 -ADE -H1' " and "A -4 -ADE -N3 " only 0.10 A apart NBONDS: found 24212 intra-atom interactions NBONDS: found 22020 intra-atom interactions NBONDS: found 20690 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0000 ----------------------- | Etotal =0.18E+07 grad(E)=1509.026 E(BOND)=634514.516 E(ANGL)=285069.328 | | E(DIHE)=0.000 E(VDW )=884195.910 | ------------------------------------------------------------------------------- NBONDS: found 19328 intra-atom interactions NBONDS: found 17899 intra-atom interactions NBONDS: found 16989 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0000 ----------------------- | Etotal =974742.835 grad(E)=976.675 E(BOND)=328151.209 E(ANGL)=174399.319 | | E(DIHE)=0.000 E(VDW )=472192.307 | ------------------------------------------------------------------------------- NBONDS: found 16074 intra-atom interactions NBONDS: found 15586 intra-atom interactions NBONDS: found 15139 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0000 ----------------------- | Etotal =574907.371 grad(E)=653.784 E(BOND)=190641.262 E(ANGL)=105165.826 | | E(DIHE)=0.000 E(VDW )=279100.283 | ------------------------------------------------------------------------------- NBONDS: found 14661 intra-atom interactions NBONDS: found 14241 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =408723.658 grad(E)=437.027 E(BOND)=147186.826 E(ANGL)=71227.982 | | E(DIHE)=0.000 E(VDW )=190308.850 | ------------------------------------------------------------------------------- NBONDS: found 13852 intra-atom interactions NBONDS: found 13439 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =319145.793 grad(E)=330.399 E(BOND)=129519.257 E(ANGL)=54937.960 | | E(DIHE)=0.000 E(VDW )=134688.576 | ------------------------------------------------------------------------------- NBONDS: found 13018 intra-atom interactions NBONDS: found 12743 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =261630.995 grad(E)=286.287 E(BOND)=109685.001 E(ANGL)=41168.875 | | E(DIHE)=0.000 E(VDW )=110777.119 | ------------------------------------------------------------------------------- NBONDS: found 12413 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =227878.900 grad(E)=217.449 E(BOND)=98840.590 E(ANGL)=30515.150 | | E(DIHE)=0.000 E(VDW )=98523.159 | ------------------------------------------------------------------------------- NBONDS: found 12206 intra-atom interactions NBONDS: found 12022 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =209607.623 grad(E)=155.930 E(BOND)=92998.781 E(ANGL)=23926.225 | | E(DIHE)=0.000 E(VDW )=92682.617 | ------------------------------------------------------------------------------- NBONDS: found 11747 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =196278.133 grad(E)=132.476 E(BOND)=89710.316 E(ANGL)=18967.581 | | E(DIHE)=0.000 E(VDW )=87600.236 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =187740.037 grad(E)=121.936 E(BOND)=87308.167 E(ANGL)=16500.684 | | E(DIHE)=0.000 E(VDW )=83931.186 | ------------------------------------------------------------------------------- NBONDS: found 11447 intra-atom interactions --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =181533.118 grad(E)=86.829 E(BOND)=88160.698 E(ANGL)=13943.928 | | E(DIHE)=0.000 E(VDW )=79428.492 | ------------------------------------------------------------------------------- NBONDS: found 11111 intra-atom interactions --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =176946.646 grad(E)=90.030 E(BOND)=86581.752 E(ANGL)=12816.271 | | E(DIHE)=0.000 E(VDW )=77548.624 | ------------------------------------------------------------------------------- NBONDS: found 10844 intra-atom interactions --------------- cycle= 140 ------ stepsize= 0.0000 ----------------------- | Etotal =173003.314 grad(E)=74.762 E(BOND)=85850.951 E(ANGL)=11715.578 | | E(DIHE)=0.000 E(VDW )=75436.785 | ------------------------------------------------------------------------------- NBONDS: found 10781 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =170374.660 grad(E)=61.060 E(BOND)=84606.066 E(ANGL)=10884.591 | | E(DIHE)=0.000 E(VDW )=74884.002 | ------------------------------------------------------------------------------- --------------- cycle= 160 ------ stepsize= 0.0000 ----------------------- | Etotal =168587.206 grad(E)=52.006 E(BOND)=84418.397 E(ANGL)=10069.822 | | E(DIHE)=0.000 E(VDW )=74098.987 | ------------------------------------------------------------------------------- NBONDS: found 10635 intra-atom interactions --------------- cycle= 170 ------ stepsize= 0.0000 ----------------------- | Etotal =167226.472 grad(E)=46.966 E(BOND)=84411.352 E(ANGL)=9555.784 | | E(DIHE)=0.000 E(VDW )=73259.336 | ------------------------------------------------------------------------------- --------------- cycle= 180 ------ stepsize= 0.0000 ----------------------- | Etotal =166165.183 grad(E)=42.275 E(BOND)=83741.895 E(ANGL)=9093.100 | | E(DIHE)=0.000 E(VDW )=73330.188 | ------------------------------------------------------------------------------- --------------- cycle= 190 ------ stepsize= 0.0000 ----------------------- | Etotal =165222.981 grad(E)=39.369 E(BOND)=83529.732 E(ANGL)=8844.074 | | E(DIHE)=0.000 E(VDW )=72849.175 | ------------------------------------------------------------------------------- NBONDS: found 10530 intra-atom interactions --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =164493.224 grad(E)=33.408 E(BOND)=83658.339 E(ANGL)=8554.988 | | E(DIHE)=0.000 E(VDW )=72279.897 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>flags include impr end X-PLOR>minimize powell nstep=200 nprint=10 end POWELL: number of degrees of freedom= 2031 CODIMP: improper type-based parameters retrieved --------------- cycle= 10 ------ stepsize= 0.0000 ----------------------- | Etotal =382525.671 grad(E)=338.258 E(BOND)=87296.772 E(ANGL)=32074.971 | | E(DIHE)=0.000 E(IMPR)=183013.526 E(VDW )=80140.403 | ------------------------------------------------------------------------------- NBONDS: found 10455 intra-atom interactions --------------- cycle= 20 ------ stepsize= 0.0000 ----------------------- | Etotal =363705.835 grad(E)=159.034 E(BOND)=81648.071 E(ANGL)=39722.817 | | E(DIHE)=0.000 E(IMPR)=156891.851 E(VDW )=85443.096 | ------------------------------------------------------------------------------- NBONDS: found 10389 intra-atom interactions --------------- cycle= 30 ------ stepsize= 0.0000 ----------------------- | Etotal =354315.566 grad(E)=153.542 E(BOND)=86308.726 E(ANGL)=44233.876 | | E(DIHE)=0.000 E(IMPR)=139315.701 E(VDW )=84457.262 | ------------------------------------------------------------------------------- NBONDS: found 10297 intra-atom interactions NBONDS: found 10230 intra-atom interactions --------------- cycle= 40 ------ stepsize= 0.0000 ----------------------- | Etotal =339169.989 grad(E)=244.743 E(BOND)=91731.059 E(ANGL)=53262.010 | | E(DIHE)=0.000 E(IMPR)=108051.924 E(VDW )=86124.995 | ------------------------------------------------------------------------------- NBONDS: found 10137 intra-atom interactions NBONDS: found 10024 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =305962.261 grad(E)=283.276 E(BOND)=90071.612 E(ANGL)=47054.727 | | E(DIHE)=0.000 E(IMPR)=84727.008 E(VDW )=84108.914 | ------------------------------------------------------------------------------- NBONDS: found 9974 intra-atom interactions --------------- cycle= 60 ------ stepsize= 0.0000 ----------------------- | Etotal =279629.273 grad(E)=234.928 E(BOND)=88665.863 E(ANGL)=38090.149 | | E(DIHE)=0.000 E(IMPR)=70834.580 E(VDW )=82038.682 | ------------------------------------------------------------------------------- NBONDS: found 9972 intra-atom interactions --------------- cycle= 70 ------ stepsize= 0.0000 ----------------------- | Etotal =264034.984 grad(E)=207.790 E(BOND)=87624.351 E(ANGL)=32411.145 | | E(DIHE)=0.000 E(IMPR)=63235.204 E(VDW )=80764.285 | ------------------------------------------------------------------------------- NBONDS: found 9973 intra-atom interactions NBONDS: found 9992 intra-atom interactions --------------- cycle= 80 ------ stepsize= 0.0000 ----------------------- | Etotal =255034.696 grad(E)=190.564 E(BOND)=87815.808 E(ANGL)=30065.970 | | E(DIHE)=0.000 E(IMPR)=56023.931 E(VDW )=81128.987 | ------------------------------------------------------------------------------- NBONDS: found 9969 intra-atom interactions --------------- cycle= 90 ------ stepsize= 0.0000 ----------------------- | Etotal =245619.619 grad(E)=130.657 E(BOND)=85497.337 E(ANGL)=27463.759 | | E(DIHE)=0.000 E(IMPR)=51116.523 E(VDW )=81542.000 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =249837.099 grad(E)=691.912 E(BOND)=84412.392 E(ANGL)=27135.956 | | E(DIHE)=0.000 E(IMPR)=56418.936 E(VDW )=81869.814 | ------------------------------------------------------------------------------- --------------- cycle= 110 ------ stepsize= 0.0000 ----------------------- | Etotal =249835.540 grad(E)=694.024 E(BOND)=84414.453 E(ANGL)=27136.682 | | E(DIHE)=0.000 E(IMPR)=56415.144 E(VDW )=81869.262 | ------------------------------------------------------------------------------- --------------- cycle= 120 ------ stepsize= 0.0000 ----------------------- | Etotal =243490.868 grad(E)=118.126 E(BOND)=84414.456 E(ANGL)=27136.683 | | E(DIHE)=0.000 E(IMPR)=50070.469 E(VDW )=81869.261 | ------------------------------------------------------------------------------- --------------- cycle= 130 ------ stepsize= 0.0000 ----------------------- | Etotal =243490.868 grad(E)=118.126 E(BOND)=84414.455 E(ANGL)=27136.683 | | E(DIHE)=0.000 E(IMPR)=50070.468 E(VDW )=81869.261 | ------------------------------------------------------------------------------- %POWELL-ERR: Line search abandoned POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>dynamics verlet DYNAmics> nstep=200 DYNAmics> timestep=0.001 ! default DYNAmics> iasvel=maxwell DYNAmics> firsttemp=300 DYNAmics> tcoupling=true DYNAmics> tbath=300 DYNAmics> nprint=50 DYNAmics> iprfrq=0 DYNAmics>end DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 0.103201372E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 33.90000 0.50416 0.49381 velocity [A/ps] : 0.07913 -0.06994 0.06286 ang. mom. [amu A/ps] : -10977.85544 40685.38433 88113.98365 kin. ener. [Kcal/mol] : 1.22200 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 33.90000 0.50416 0.49381 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)=244084.641 E(kin)=593.773 temperature=294.240 | | Etotal =243490.868 grad(E)=118.126 E(BOND)=84414.455 E(ANGL)=27136.683 | | E(DIHE)=0.000 E(IMPR)=50070.468 E(VDW )=81869.261 | ------------------------------------------------------------------------------- NBONDS: found 9939 intra-atom interactions NBONDS: found 9900 intra-atom interactions NBONDS: found 9905 intra-atom interactions --------------- step= 50 at 0.05000 ps -------------------------------- | E(kin)+E(total)=232678.262 E(kin)=4322.080 temperature=2141.772 | | Etotal =228356.182 grad(E)=112.365 E(BOND)=84469.529 E(ANGL)=21482.917 | | E(DIHE)=0.000 E(IMPR)=43066.828 E(VDW )=79336.909 | ------------------------------------------------------------------------------- NBONDS: found 9888 intra-atom interactions NBONDS: found 9874 intra-atom interactions --------------- step= 100 at 0.10000 ps -------------------------------- | E(kin)+E(total)=222378.286 E(kin)=1389.757 temperature=688.683 | | Etotal =220988.529 grad(E)=65.162 E(BOND)=84258.972 E(ANGL)=18648.950 | | E(DIHE)=0.000 E(IMPR)=40581.958 E(VDW )=77498.650 | ------------------------------------------------------------------------------- NBONDS: found 9862 intra-atom interactions NBONDS: found 9834 intra-atom interactions --------------- step= 150 at 0.15000 ps -------------------------------- | E(kin)+E(total)=218224.379 E(kin)=1636.884 temperature=811.145 | | Etotal =216587.495 grad(E)=74.929 E(BOND)=84416.220 E(ANGL)=18426.217 | | E(DIHE)=0.000 E(IMPR)=36683.256 E(VDW )=77061.802 | ------------------------------------------------------------------------------- NBONDS: found 9823 intra-atom interactions NBONDS: found 9795 intra-atom interactions --------------- step= 200 at 0.20000 ps -------------------------------- | E(kin)+E(total)=213902.718 E(kin)=2072.351 temperature=1026.937 | | Etotal =211830.367 grad(E)=71.269 E(BOND)=83805.990 E(ANGL)=17922.984 | | E(DIHE)=0.000 E(IMPR)=32930.296 E(VDW )=77171.097 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 33.90000 0.50416 0.49381 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> X-PLOR>parameter PARRDR> nbonds NBDSET> rconst=2 NBDSET> nbxmod=-3 NBDSET> repel=0.75 ! Repulsive non-bonded energy only NBDSET> end PARRDR>end X-PLOR> X-PLOR>minimize powell nstep=400 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=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 8498 intra-atom interactions NBONDS: found 9272 intra-atom interactions NBONDS: found 9947 intra-atom interactions --------------- cycle= 25 ------ stepsize= 0.0000 ----------------------- | Etotal =39603.519 grad(E)=205.402 E(BOND)=6682.217 E(ANGL)=20549.336 | | E(DIHE)=0.000 E(IMPR)=12147.206 E(VDW )=224.759 | ------------------------------------------------------------------------------- NBONDS: found 10454 intra-atom interactions NBONDS: found 10763 intra-atom interactions NBONDS: found 10940 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =14794.551 grad(E)=134.046 E(BOND)=1900.607 E(ANGL)=7760.823 | | E(DIHE)=0.000 E(IMPR)=4625.459 E(VDW )=507.662 | ------------------------------------------------------------------------------- NBONDS: found 10981 intra-atom interactions --------------- cycle= 75 ------ stepsize= 0.0001 ----------------------- | Etotal =6561.761 grad(E)=93.968 E(BOND)=475.331 E(ANGL)=4496.416 | | E(DIHE)=0.000 E(IMPR)=1186.273 E(VDW )=403.740 | ------------------------------------------------------------------------------- NBONDS: found 11004 intra-atom interactions NBONDS: found 11000 intra-atom interactions --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =3252.956 grad(E)=39.572 E(BOND)=252.414 E(ANGL)=2013.528 | | E(DIHE)=0.000 E(IMPR)=615.182 E(VDW )=371.831 | ------------------------------------------------------------------------------- --------------- cycle= 125 ------ stepsize= 0.0001 ----------------------- | Etotal =2319.686 grad(E)=25.279 E(BOND)=183.750 E(ANGL)=1360.790 | | E(DIHE)=0.000 E(IMPR)=422.930 E(VDW )=352.217 | ------------------------------------------------------------------------------- NBONDS: found 11151 intra-atom interactions --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =1536.496 grad(E)=25.221 E(BOND)=135.499 E(ANGL)=799.919 | | E(DIHE)=0.000 E(IMPR)=208.012 E(VDW )=393.066 | ------------------------------------------------------------------------------- NBONDS: found 11312 intra-atom interactions --------------- cycle= 175 ------ stepsize= 0.0001 ----------------------- | Etotal =1139.845 grad(E)=16.552 E(BOND)=74.266 E(ANGL)=549.721 | | E(DIHE)=0.000 E(IMPR)=103.325 E(VDW )=412.533 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =943.457 grad(E)=14.297 E(BOND)=64.381 E(ANGL)=447.145 | | E(DIHE)=0.000 E(IMPR)=79.673 E(VDW )=352.258 | ------------------------------------------------------------------------------- --------------- cycle= 225 ------ stepsize= 0.0001 ----------------------- | Etotal =785.609 grad(E)=7.220 E(BOND)=49.487 E(ANGL)=391.563 | | E(DIHE)=0.000 E(IMPR)=59.609 E(VDW )=284.951 | ------------------------------------------------------------------------------- --------------- cycle= 250 ------ stepsize= 0.0000 ----------------------- | Etotal =699.213 grad(E)=8.840 E(BOND)=44.138 E(ANGL)=367.490 | | E(DIHE)=0.000 E(IMPR)=52.009 E(VDW )=235.576 | ------------------------------------------------------------------------------- NBONDS: found 11462 intra-atom interactions --------------- cycle= 275 ------ stepsize= 0.0001 ----------------------- | Etotal =615.696 grad(E)=9.481 E(BOND)=38.099 E(ANGL)=331.633 | | E(DIHE)=0.000 E(IMPR)=42.997 E(VDW )=202.967 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0000 ----------------------- | Etotal =546.664 grad(E)=9.330 E(BOND)=31.086 E(ANGL)=286.255 | | E(DIHE)=0.000 E(IMPR)=43.124 E(VDW )=186.199 | ------------------------------------------------------------------------------- --------------- cycle= 325 ------ stepsize= 0.0001 ----------------------- | Etotal =481.337 grad(E)=5.780 E(BOND)=28.005 E(ANGL)=237.971 | | E(DIHE)=0.000 E(IMPR)=40.134 E(VDW )=175.227 | ------------------------------------------------------------------------------- NBONDS: found 11601 intra-atom interactions --------------- cycle= 350 ------ stepsize= 0.0000 ----------------------- | Etotal =429.253 grad(E)=7.112 E(BOND)=26.608 E(ANGL)=206.917 | | E(DIHE)=0.000 E(IMPR)=32.397 E(VDW )=163.331 | ------------------------------------------------------------------------------- --------------- cycle= 375 ------ stepsize= 0.0001 ----------------------- | Etotal =385.805 grad(E)=7.722 E(BOND)=21.805 E(ANGL)=182.243 | | E(DIHE)=0.000 E(IMPR)=27.238 E(VDW )=154.519 | ------------------------------------------------------------------------------- --------------- cycle= 400 ------ stepsize= 0.0000 ----------------------- | Etotal =357.893 grad(E)=5.159 E(BOND)=20.482 E(ANGL)=173.050 | | E(DIHE)=0.000 E(IMPR)=23.383 E(VDW )=140.977 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>dynamics verlet DYNAmics> nstep=1000 DYNAmics> timestep=0.005 DYNAmics> iasvel=maxwell DYNAmics> firsttemp=300 DYNAmics> tcoupling=true DYNAmics> tbath=300 DYNAmics> nprint=100 DYNAmics> iprfrq=0 DYNAmics>end DYNAMC: number of degrees of freedom= 2031 ASSVEL: velocities assigned at 300.0000 K, SEED= 0.136413942E+10 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 33.90000 0.50416 0.49381 velocity [A/ps] : 0.01534 -0.00112 0.04460 ang. mom. [amu A/ps] : -19005.11593-110948.98874 -22846.36445 kin. ener. [Kcal/mol] : 0.18004 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 33.90000 0.50416 0.49381 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)=984.632 E(kin)=626.740 temperature=310.576 | | Etotal =357.893 grad(E)=5.159 E(BOND)=20.482 E(ANGL)=173.050 | | E(DIHE)=0.000 E(IMPR)=23.383 E(VDW )=140.977 | ------------------------------------------------------------------------------- --------------- step= 100 at 0.50000 ps -------------------------------- | E(kin)+E(total)=13805.585 E(kin)=1967.820 temperature=975.137 | | Etotal =11837.765 grad(E)=559.473 E(BOND)=1256.329 E(ANGL)=2026.322 | | E(DIHE)=0.000 E(IMPR)=8434.662 E(VDW )=120.452 | ------------------------------------------------------------------------------- --------------- step= 200 at 1.00000 ps -------------------------------- | E(kin)+E(total)=11159.637 E(kin)=2149.763 temperature=1065.298 | | Etotal =9009.874 grad(E)=472.379 E(BOND)=1125.408 E(ANGL)=1825.279 | | E(DIHE)=0.000 E(IMPR)=5946.220 E(VDW )=112.968 | ------------------------------------------------------------------------------- --------------- step= 300 at 1.50000 ps -------------------------------- | E(kin)+E(total)=15746.166 E(kin)=1701.668 temperature=843.248 | | Etotal =14044.498 grad(E)=630.642 E(BOND)=1133.481 E(ANGL)=1693.330 | | E(DIHE)=0.000 E(IMPR)=11113.651 E(VDW )=104.036 | ------------------------------------------------------------------------------- NBONDS: found 11731 intra-atom interactions --------------- step= 400 at 2.00000 ps -------------------------------- | E(kin)+E(total)=14605.733 E(kin)=2588.366 temperature=1282.644 | | Etotal =12017.367 grad(E)=562.090 E(BOND)=1364.104 E(ANGL)=2017.906 | | E(DIHE)=0.000 E(IMPR)=8542.866 E(VDW )=92.491 | ------------------------------------------------------------------------------- --------------- step= 500 at 2.50000 ps -------------------------------- | E(kin)+E(total)=17780.934 E(kin)=2108.690 temperature=1044.944 | | Etotal =15672.244 grad(E)=656.684 E(BOND)=955.526 E(ANGL)=1646.836 | | E(DIHE)=0.000 E(IMPR)=12984.110 E(VDW )=85.773 | ------------------------------------------------------------------------------- --------------- step= 600 at 3.00000 ps -------------------------------- | E(kin)+E(total)=13900.573 E(kin)=2038.830 temperature=1010.326 | | Etotal =11861.743 grad(E)=558.457 E(BOND)=1133.781 E(ANGL)=1580.230 | | E(DIHE)=0.000 E(IMPR)=9068.719 E(VDW )=79.013 | ------------------------------------------------------------------------------- --------------- step= 700 at 3.50000 ps -------------------------------- | E(kin)+E(total)=15392.097 E(kin)=2101.786 temperature=1041.523 | | Etotal =13290.311 grad(E)=587.512 E(BOND)=1355.874 E(ANGL)=1911.368 | | E(DIHE)=0.000 E(IMPR)=9940.132 E(VDW )=82.938 | ------------------------------------------------------------------------------- --------------- step= 800 at 4.00000 ps -------------------------------- | E(kin)+E(total)=13283.278 E(kin)=2448.458 temperature=1213.314 | | Etotal =10834.821 grad(E)=524.642 E(BOND)=1311.011 E(ANGL)=1797.561 | | E(DIHE)=0.000 E(IMPR)=7657.852 E(VDW )=68.396 | ------------------------------------------------------------------------------- --------------- step= 900 at 4.50000 ps -------------------------------- | E(kin)+E(total)=16860.615 E(kin)=2625.581 temperature=1301.086 | | Etotal =14235.034 grad(E)=614.374 E(BOND)=1568.595 E(ANGL)=2029.284 | | E(DIHE)=0.000 E(IMPR)=10567.501 E(VDW )=69.654 | ------------------------------------------------------------------------------- --------------- step= 1000 at 5.00000 ps -------------------------------- | E(kin)+E(total)=13075.690 E(kin)=2202.284 temperature=1091.324 | | Etotal =10873.405 grad(E)=508.976 E(BOND)=1488.091 E(ANGL)=1963.245 | | E(DIHE)=0.000 E(IMPR)=7357.252 E(VDW )=64.817 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 33.90000 0.50416 0.49381 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> X-PLOR>! H-building won't actually place protons, since we're using a fully protonated X-PLOR>! topology/parameter set, but it may improve their positions X-PLOR>! We're using "nbonds repel", so the "elec" flag is irrelevant X-PLOR> X-PLOR>flags exclude vdw end X-PLOR>vector do (mass=1) (name h*) SELRPN: 230 atoms have been selected out of 677 X-PLOR>hbuild selection=(name h*) phistep=360 end SELRPN: 230 atoms have been selected out of 677 HBUILD: dihedral PHI STePs for spin = 360.0000 HBUILD: cutoff during water acceptor search = 7.5000 HBUILD: H5' ,H5'', placed for donor A 1 GUA C5' . HBUILD: H4' , , placed for donor A 1 GUA C4' . HBUILD: H1' , , placed for donor A 1 GUA C1' . HBUILD: H1 , , placed for donor A 1 GUA N1 . HBUILD: H8 , , placed for donor A 1 GUA C8 . HBUILD: H2' , , placed for donor A 1 GUA C2' . HBUILD: H3' , , placed for donor A 1 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 2 GUA C5' . HBUILD: H4' , , placed for donor A 2 GUA C4' . HBUILD: H1' , , placed for donor A 2 GUA C1' . HBUILD: H1 , , placed for donor A 2 GUA N1 . HBUILD: H8 , , placed for donor A 2 GUA C8 . HBUILD: H2' , , placed for donor A 2 GUA C2' . HBUILD: H3' , , placed for donor A 2 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 3 CYT C5' . HBUILD: H4' , , placed for donor A 3 CYT C4' . HBUILD: H1' , , placed for donor A 3 CYT C1' . HBUILD: H6 , , placed for donor A 3 CYT C6 . HBUILD: H5 , , placed for donor A 3 CYT C5 . HBUILD: H2' , , placed for donor A 3 CYT C2' . HBUILD: H3' , , placed for donor A 3 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 4 ADE C5' . HBUILD: H4' , , placed for donor A 4 ADE C4' . HBUILD: H1' , , placed for donor A 4 ADE C1' . HBUILD: H2 , , placed for donor A 4 ADE C2 . HBUILD: H8 , , placed for donor A 4 ADE C8 . HBUILD: H2' , , placed for donor A 4 ADE C2' . HBUILD: H3' , , placed for donor A 4 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 5 GUA C5' . HBUILD: H4' , , placed for donor A 5 GUA C4' . HBUILD: H1' , , placed for donor A 5 GUA C1' . HBUILD: H1 , , placed for donor A 5 GUA N1 . HBUILD: H8 , , placed for donor A 5 GUA C8 . HBUILD: H2' , , placed for donor A 5 GUA C2' . HBUILD: H3' , , placed for donor A 5 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 6 GUA C5' . HBUILD: H4' , , placed for donor A 6 GUA C4' . HBUILD: H1' , , placed for donor A 6 GUA C1' . HBUILD: H1 , , placed for donor A 6 GUA N1 . HBUILD: H8 , , placed for donor A 6 GUA C8 . HBUILD: H2' , , placed for donor A 6 GUA C2' . HBUILD: H3' , , placed for donor A 6 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 7 GUA C5' . HBUILD: H4' , , placed for donor A 7 GUA C4' . HBUILD: H1' , , placed for donor A 7 GUA C1' . HBUILD: H1 , , placed for donor A 7 GUA N1 . HBUILD: H8 , , placed for donor A 7 GUA C8 . HBUILD: H2' , , placed for donor A 7 GUA C2' . HBUILD: H3' , , placed for donor A 7 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 8 CYT C5' . HBUILD: H4' , , placed for donor A 8 CYT C4' . HBUILD: H1' , , placed for donor A 8 CYT C1' . HBUILD: H6 , , placed for donor A 8 CYT C6 . HBUILD: H5 , , placed for donor A 8 CYT C5 . HBUILD: H2' , , placed for donor A 8 CYT C2' . HBUILD: H3' , , placed for donor A 8 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 9 URI C5' . HBUILD: H4' , , placed for donor A 9 URI C4' . HBUILD: H1' , , placed for donor A 9 URI C1' . HBUILD: H6 , , placed for donor A 9 URI C6 . HBUILD: H3 , , placed for donor A 9 URI N3 . HBUILD: H5 , , placed for donor A 9 URI C5 . HBUILD: H2' , , placed for donor A 9 URI C2' . HBUILD: H3' , , placed for donor A 9 URI C3' . HBUILD: H5' ,H5'', placed for donor A 10 CYT C5' . HBUILD: H4' , , placed for donor A 10 CYT C4' . HBUILD: H1' , , placed for donor A 10 CYT C1' . HBUILD: H6 , , placed for donor A 10 CYT C6 . HBUILD: H5 , , placed for donor A 10 CYT C5 . HBUILD: H2' , , placed for donor A 10 CYT C2' . HBUILD: H3' , , placed for donor A 10 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 11 ADE C5' . HBUILD: H4' , , placed for donor A 11 ADE C4' . HBUILD: H1' , , placed for donor A 11 ADE C1' . HBUILD: H2 , , placed for donor A 11 ADE C2 . HBUILD: H8 , , placed for donor A 11 ADE C8 . HBUILD: H2' , , placed for donor A 11 ADE C2' . HBUILD: H3' , , placed for donor A 11 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 12 URI C5' . HBUILD: H4' , , placed for donor A 12 URI C4' . HBUILD: H1' , , placed for donor A 12 URI C1' . HBUILD: H6 , , placed for donor A 12 URI C6 . HBUILD: H3 , , placed for donor A 12 URI N3 . HBUILD: H5 , , placed for donor A 12 URI C5 . HBUILD: H2' , , placed for donor A 12 URI C2' . HBUILD: H3' , , placed for donor A 12 URI C3' . HBUILD: H5' ,H5'', placed for donor A 13 ADE C5' . HBUILD: H4' , , placed for donor A 13 ADE C4' . HBUILD: H1' , , placed for donor A 13 ADE C1' . HBUILD: H2 , , placed for donor A 13 ADE C2 . HBUILD: H8 , , placed for donor A 13 ADE C8 . HBUILD: H2' , , placed for donor A 13 ADE C2' . HBUILD: H3' , , placed for donor A 13 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 14 ADE C5' . HBUILD: H4' , , placed for donor A 14 ADE C4' . HBUILD: H1' , , placed for donor A 14 ADE C1' . HBUILD: H2 , , placed for donor A 14 ADE C2 . HBUILD: H8 , , placed for donor A 14 ADE C8 . HBUILD: H2' , , placed for donor A 14 ADE C2' . HBUILD: H3' , , placed for donor A 14 ADE C3' . HBUILD: H5' ,H5'', placed for donor A 15 CYT C5' . HBUILD: H4' , , placed for donor A 15 CYT C4' . HBUILD: H1' , , placed for donor A 15 CYT C1' . HBUILD: H6 , , placed for donor A 15 CYT C6 . HBUILD: H5 , , placed for donor A 15 CYT C5 . HBUILD: H2' , , placed for donor A 15 CYT C2' . HBUILD: H3' , , placed for donor A 15 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 16 CYT C5' . HBUILD: H4' , , placed for donor A 16 CYT C4' . HBUILD: H1' , , placed for donor A 16 CYT C1' . HBUILD: H6 , , placed for donor A 16 CYT C6 . HBUILD: H5 , , placed for donor A 16 CYT C5 . HBUILD: H2' , , placed for donor A 16 CYT C2' . HBUILD: H3' , , placed for donor A 16 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 17 CYT C5' . HBUILD: H4' , , placed for donor A 17 CYT C4' . HBUILD: H1' , , placed for donor A 17 CYT C1' . HBUILD: H6 , , placed for donor A 17 CYT C6 . HBUILD: H5 , , placed for donor A 17 CYT C5 . HBUILD: H2' , , placed for donor A 17 CYT C2' . HBUILD: H3' , , placed for donor A 17 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 18 URI C5' . HBUILD: H4' , , placed for donor A 18 URI C4' . HBUILD: H1' , , placed for donor A 18 URI C1' . HBUILD: H6 , , placed for donor A 18 URI C6 . HBUILD: H3 , , placed for donor A 18 URI N3 . HBUILD: H5 , , placed for donor A 18 URI C5 . HBUILD: H2' , , placed for donor A 18 URI C2' . HBUILD: H3' , , placed for donor A 18 URI C3' . HBUILD: H5' ,H5'', placed for donor A 19 GUA C5' . HBUILD: H4' , , placed for donor A 19 GUA C4' . HBUILD: H1' , , placed for donor A 19 GUA C1' . HBUILD: H1 , , placed for donor A 19 GUA N1 . HBUILD: H8 , , placed for donor A 19 GUA C8 . HBUILD: H2' , , placed for donor A 19 GUA C2' . HBUILD: H3' , , placed for donor A 19 GUA C3' . HBUILD: H5' ,H5'', placed for donor A 20 CYT C5' . HBUILD: H4' , , placed for donor A 20 CYT C4' . HBUILD: H1' , , placed for donor A 20 CYT C1' . HBUILD: H6 , , placed for donor A 20 CYT C6 . HBUILD: H5 , , placed for donor A 20 CYT C5 . HBUILD: H2' , , placed for donor A 20 CYT C2' . HBUILD: H3' , , placed for donor A 20 CYT C3' . HBUILD: H5' ,H5'', placed for donor A 21 CYT C5' . HBUILD: H4' , , placed for donor A 21 CYT C4' . HBUILD: H1' , , placed for donor A 21 CYT C1' . HBUILD: H6 , , placed for donor A 21 CYT C6 . HBUILD: H5 , , placed for donor A 21 CYT C5 . HBUILD: H2' , , placed for donor A 21 CYT C2' . HBUILD: H3' , , placed for donor A 21 CYT C3' . HBUILD: H5T , , , constructed (spin) for donor A 1 GUA O5T . HBUILD: H21 ,H22 , , constructed (spin) for donor A 1 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 1 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 2 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 2 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 3 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 3 CYT O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 4 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 4 ADE O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 5 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 5 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 6 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 6 GUA O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 7 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 7 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 8 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 8 CYT O2' . HBUILD: HO2', , , constructed (spin) for donor A 9 URI O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 10 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 10 CYT O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 11 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 11 ADE O2' . HBUILD: HO2', , , constructed (spin) for donor A 12 URI O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 13 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 13 ADE O2' . HBUILD: H61 ,H62 , , constructed (spin) for donor A 14 ADE N6 . HBUILD: HO2', , , constructed (spin) for donor A 14 ADE O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 15 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 15 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 16 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 16 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 17 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 17 CYT O2' . HBUILD: HO2', , , constructed (spin) for donor A 18 URI O2' . HBUILD: H21 ,H22 , , constructed (spin) for donor A 19 GUA N2 . HBUILD: HO2', , , constructed (spin) for donor A 19 GUA O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 20 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 20 CYT O2' . HBUILD: H41 ,H42 , , constructed (spin) for donor A 21 CYT N4 . HBUILD: HO2', , , constructed (spin) for donor A 21 CYT O2' . HBUILD: H3T , , , constructed (spin) for donor A 21 CYT O3' . X-PLOR> X-PLOR>flags include vdw end X-PLOR>minimize powell nstep=800 nprint=50 end POWELL: number of degrees of freedom= 2031 NBONDS: generating intra-molecular exclusion list with mode=-3 MAKINB: mode -3 found 2027 exclusions and 0 interactions(1-4) NBONDS: found 11711 intra-atom interactions NBONDS: found 11729 intra-atom interactions NBONDS: found 11746 intra-atom interactions --------------- cycle= 50 ------ stepsize= 0.0000 ----------------------- | Etotal =426.341 grad(E)=21.773 E(BOND)=31.460 E(ANGL)=151.681 | | E(DIHE)=0.000 E(IMPR)=144.266 E(VDW )=98.934 | ------------------------------------------------------------------------------- --------------- cycle= 100 ------ stepsize= 0.0000 ----------------------- | Etotal =223.320 grad(E)=4.243 E(BOND)=11.633 E(ANGL)=109.393 | | E(DIHE)=0.000 E(IMPR)=17.715 E(VDW )=84.579 | ------------------------------------------------------------------------------- --------------- cycle= 150 ------ stepsize= 0.0000 ----------------------- | Etotal =197.974 grad(E)=2.674 E(BOND)=10.771 E(ANGL)=105.209 | | E(DIHE)=0.000 E(IMPR)=14.674 E(VDW )=67.318 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.0000 ----------------------- | Etotal =182.992 grad(E)=2.559 E(BOND)=9.931 E(ANGL)=101.142 | | E(DIHE)=0.000 E(IMPR)=15.006 E(VDW )=56.913 | ------------------------------------------------------------------------------- NBONDS: found 11708 intra-atom interactions --------------- cycle= 250 ------ stepsize= 0.0000 ----------------------- | Etotal =170.759 grad(E)=2.687 E(BOND)=9.041 E(ANGL)=95.196 | | E(DIHE)=0.000 E(IMPR)=14.556 E(VDW )=51.966 | ------------------------------------------------------------------------------- --------------- cycle= 300 ------ stepsize= 0.0000 ----------------------- | Etotal =156.073 grad(E)=2.640 E(BOND)=8.243 E(ANGL)=87.921 | | E(DIHE)=0.000 E(IMPR)=14.107 E(VDW )=45.802 | ------------------------------------------------------------------------------- NBONDS: found 11734 intra-atom interactions --------------- cycle= 350 ------ stepsize= 0.0000 ----------------------- | Etotal =143.349 grad(E)=2.545 E(BOND)=7.931 E(ANGL)=83.207 | | E(DIHE)=0.000 E(IMPR)=13.931 E(VDW )=38.279 | ------------------------------------------------------------------------------- --------------- cycle= 400 ------ stepsize= 0.0000 ----------------------- | Etotal =134.185 grad(E)=2.534 E(BOND)=7.171 E(ANGL)=80.271 | | E(DIHE)=0.000 E(IMPR)=13.194 E(VDW )=33.548 | ------------------------------------------------------------------------------- --------------- cycle= 450 ------ stepsize= 0.0000 ----------------------- | Etotal =125.050 grad(E)=1.562 E(BOND)=6.219 E(ANGL)=78.090 | | E(DIHE)=0.000 E(IMPR)=11.773 E(VDW )=28.967 | ------------------------------------------------------------------------------- --------------- cycle= 500 ------ stepsize= 0.0000 ----------------------- | Etotal =120.671 grad(E)=1.355 E(BOND)=5.985 E(ANGL)=76.157 | | E(DIHE)=0.000 E(IMPR)=11.322 E(VDW )=27.207 | ------------------------------------------------------------------------------- --------------- cycle= 550 ------ stepsize= 0.0000 ----------------------- | Etotal =116.324 grad(E)=1.193 E(BOND)=5.972 E(ANGL)=75.559 | | E(DIHE)=0.000 E(IMPR)=11.002 E(VDW )=23.790 | ------------------------------------------------------------------------------- --------------- cycle= 600 ------ stepsize= 0.0000 ----------------------- | Etotal =111.464 grad(E)=1.402 E(BOND)=5.630 E(ANGL)=74.305 | | E(DIHE)=0.000 E(IMPR)=10.717 E(VDW )=20.813 | ------------------------------------------------------------------------------- --------------- cycle= 650 ------ stepsize= 0.0000 ----------------------- | Etotal =107.850 grad(E)=1.341 E(BOND)=5.365 E(ANGL)=72.967 | | E(DIHE)=0.000 E(IMPR)=10.448 E(VDW )=19.070 | ------------------------------------------------------------------------------- NBONDS: found 11638 intra-atom interactions --------------- cycle= 700 ------ stepsize= 0.0000 ----------------------- | Etotal =105.245 grad(E)=1.108 E(BOND)=5.066 E(ANGL)=71.046 | | E(DIHE)=0.000 E(IMPR)=10.543 E(VDW )=18.590 | ------------------------------------------------------------------------------- --------------- cycle= 750 ------ stepsize= 0.0000 ----------------------- | Etotal =102.753 grad(E)=1.060 E(BOND)=4.957 E(ANGL)=70.128 | | E(DIHE)=0.000 E(IMPR)=10.181 E(VDW )=17.488 | ------------------------------------------------------------------------------- --------------- cycle= 800 ------ stepsize= 0.0000 ----------------------- | Etotal =101.201 grad(E)=0.848 E(BOND)=4.765 E(ANGL)=69.335 | | E(DIHE)=0.000 E(IMPR)=9.907 E(VDW )=17.193 | ------------------------------------------------------------------------------- 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>! Total energy should be no more than about 100. If it is, it is probably X-PLOR>! because one or more purines are trapped in a crumpled conformation. X-PLOR> X-PLOR>flags exclude * include bond angle dihe impr vdw end 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 $RMS_BOND set to 0.163188E-02 (real) X-PLOR>evaluate ($v_bond=$violations) EVALUATE: symbol $V_BOND set to 0.000000E+00 (real) X-PLOR>print threshold=5 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. Number of violations greater 5.000: 0 RMS deviation= 0.590 X-PLOR>evaluate ($rms_angl=$result) EVALUATE: symbol $RMS_ANGL set to 0.589754 (real) X-PLOR>evaluate ($v_angl=$violations) EVALUATE: symbol $V_ANGL set to 0.000000E+00 (real) X-PLOR>print threshold=15 dihedrals CODDIH: dihedral type-based parameters retrieved (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 15.000: 0 X-PLOR>evaluate ($rms_dihe=$result) EVALUATE: symbol $RMS_DIHE set to 0.000000E+00 (real) X-PLOR>evaluate ($v_dihe=$violations) EVALUATE: symbol $V_DIHE set to 0.000000E+00 (real) X-PLOR>print threshold=5 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 5.000: 0 RMS deviation= 0.268 X-PLOR>evaluate ($rms_impr=$result) EVALUATE: symbol $RMS_IMPR set to 0.268477 (real) X-PLOR>evaluate ($v_impr=$violations) EVALUATE: symbol $V_IMPR set to 0.000000E+00 (real) X-PLOR> X-PLOR>set echo=off message=off end Energy: bond 4.76534, angle 69.3348, dihedral 0, improper 9.90696, VdW 17.1935, total 101.201 RMSD: bond 1.631883E-03, angle 0.589754, dihedral 0, improper 0.268477 Violations: bond 0, angle 0, dihedral 0, improper 0 X-PLOR> X-PLOR>write coordinates output=template.pdb end ASSFIL: file /sgi/people/dcs/ws/xplor/italy2.4x/template.pdb opened. X-PLOR> X-PLOR>stop CSTACK: size= 200000 used= 227 current= 0 HEAP: maximum use= 98626 current use= 0 X-PLOR: total CPU time= 44.1084 s X-PLOR: entry time at 13:41:23 27-Apr-96 X-PLOR: exit time at 13:42:09 27-Apr-96