XPLOR-NIH version 2.9.5 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: [unknown] on: x86/Linux at: 04-Jun-04 10:27:31 X-PLOR>remarks +++++++++++++++HBUILDTES+++++++++++++++++++++++++++++++++++++ X-PLOR>remarks Test run for the hydrogen position builder including waters X-PLOR>remarks by Axel Brunger 1982/83 X-PLOR> X-PLOR>rtf @TOPPAR:toph11.pro @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pro opened. RTFRDR>REMARKS TOPH11.PRO ( from TOPH10.INP) RTFRDR>REMARKS ============================= RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. RTFRDR>REMARKS DNA/RNA atoms appended . RTFRDR>REMARKS few atoms never referenced switched off. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.wat opened. RTFRDR>remarks TOPH11.WAT RTFRDR>remarks ========== RTFRDR>remarks topology file for water RTFRDR>remarks available: TIP3P model RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param11.pro @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.pro opened. PARRDR>REMARKS PARAM11.PRO ( from PARAM6A ) PARRDR>REMARKS =========== PARRDR>REMARKS PROTEIN PARAMETERS: PARRDR>REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4 PARRDR>REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL. PARRDR>REMARKS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR>REMARKS PARRDR>set echo=false end PARRDR> @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.wat opened. PARRDR>remarks PARAM11.WAT (water parameters) PARRDR>remarks =========== PARRDR>remarks available: TIPS3P model PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR> X-PLOR>segment SEGMENT> name=BET1 SEGMENT> chain CHAIN> @TOPPAR:toph11.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pep opened. CHAIN>REMARKS TOPH11-MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> PRO VAL ASN THR PHE VAL HIS MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 7 residues were inserted into segment "BET1" XPLOR: current counts (number in parenthesis is maximum) NATOM= 71(MAXA= 200) NBOND= 73(MAXB= 100) NTHETA= 107(MAXT= 200) NGRP= 28(MAXGRP= 100) NPHI= 36(MAXP= 100) NIMPHI= 40(MAXIMP= 100) NDON= 13(MAXPAD= 100) NACC= 10(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>segment SEGMENT> name=BET2 SEGMENT> chain CHAIN> @TOPPAR:toph11.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pep opened. CHAIN>REMARKS TOPH11-MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> SER ILE THR ASP CYS ARG GLU MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 7 residues were inserted into segment "BET2" XPLOR: current counts (number in parenthesis is maximum) NATOM= 143(MAXA= 200) NBOND= 144(MAXB= 200) NTHETA= 208(MAXT= 400) NGRP= 55(MAXGRP= 100) NPHI= 79(MAXP= 100) NIMPHI= 66(MAXIMP= 100) NDON= 29(MAXPAD= 100) NACC= 24(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>segment SEGMENT> name=TIP3 SEGMENT> molecule MOLECULE> name=TIP3 number=5 MOLECULE> end SEGMENT>end SEGMNT: 5 residues were inserted into segment "TIP3" XPLOR: current counts (number in parenthesis is maximum) NATOM= 158(MAXA= 200) NBOND= 154(MAXB= 200) NTHETA= 213(MAXT= 400) NGRP= 60(MAXGRP= 100) NPHI= 79(MAXP= 100) NIMPHI= 66(MAXIMP= 100) NDON= 29(MAXPAD= 100) NACC= 24(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>coor COOR> remarks coordinates obtained from Greg Petsko COOR> remarks neutron diffraction structure of ribonuclease COOR> natoms=158 COOR> 1 1 PRO HT1 27.19210 7.94321 7.45578 BET1 1 0.00000 X-PLOR> X-PLOR> X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR>! X-PLOR>coor initial selection=( hydrogen ) end SELRPN: 39 atoms have been selected out of 158 COOR: using atom subset. COOR: selected main coordinates initialized X-PLOR> X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=4.7 doff=5.2 dcut=11.5 aon=50.0 aoff=70.0 acut=180.0 HBDSET> tolerance=3.0 !! tolerance for hbuild HBDSET> end PARRDR> nbonds NBDSET> atom cdie shift eps=1.0 NBDSET> cutnb=13.5 ctonnb=6.5 ctofnb=7.5 NBDSET> nbxmod=5 vswitch tolerance=3.0 !! increase tolerance for hbuild NBDSET> end PARRDR>end X-PLOR> X-PLOR>flags exclude * include dihe elec vdw hbon end X-PLOR> X-PLOR>hbuild HBUILD> selection=( hydrogen and not segid TIP3 ) SELRPN: 29 atoms have been selected out of 158 HBUILD> print=true phistp=10.0 cutwat=5.7 HBUILD>end HBUILD: dihedral PHI STePs for spin = 10.0000 HBUILD: cutoff during water acceptor search = 5.7000 HBUILD: HT1 ,HT2 , placed for donor BET1 1 PRO N . HBUILD: H , , placed for donor BET1 2 VAL N . HBUILD: H , , placed for donor BET1 3 ASN N . HBUILD: H , , placed for donor BET1 4 THR N . HBUILD: H , , placed for donor BET1 5 PHE N . HBUILD: H , , placed for donor BET1 6 VAL N . HBUILD: H , , placed for donor BET1 7 HIS N . HBUILD: HD1 , , placed for donor BET1 7 HIS ND1 . HBUILD: HE2 , , placed for donor BET1 7 HIS NE2 . HBUILD: H , , placed for donor BET2 2 ILE N . HBUILD: H , , placed for donor BET2 3 THR N . HBUILD: H , , placed for donor BET2 4 ASP N . HBUILD: H , , placed for donor BET2 5 CYS N . HBUILD: H , , placed for donor BET2 6 ARG N . HBUILD: HE , , placed for donor BET2 6 ARG NE . HBUILD: H , , placed for donor BET2 7 GLU N . MAKINB: mode 5 found 9 exclusions, 4 interactions(1-4) and 5 GB exclusions HBONDS: allocating space for 333 h-bond interactions. HBONDS: 16 distance exclusions and 0 angle exclusions HBONDS: 645 fixed h-bonds, currently 32 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 0.000 -0.693 -26.264 -26.957 10.0 0.000 0.495 -0.663 -26.153 -26.322 20.0 0.000 1.918 -0.644 -26.018 -24.744 30.0 0.000 4.100 -0.647 -25.878 -22.425 40.0 0.000 6.776 -0.676 -25.745 -19.645 50.0 0.000 9.624 -0.727 -25.631 -16.734 60.0 0.000 12.300 -0.785 -25.549 -14.034 70.0 0.000 14.482 -0.837 -25.509 -11.865 80.0 0.000 15.905 -0.874 -25.522 -10.491 90.0 0.000 16.400 -0.892 -25.586 -10.078 100.0 -0.002 15.905 -0.894 -25.684 -10.674 110.0 -0.007 14.482 -0.884 -25.793 -12.203 120.0 -0.017 12.300 -0.866 -25.894 -14.476 130.0 -0.024 9.624 -0.843 -25.974 -17.218 140.0 -0.023 6.776 -0.819 -26.026 -20.093 150.0 -0.012 4.100 -0.794 -26.047 -22.753 160.0 -0.001 1.918 -0.768 -26.050 -24.900 170.0 0.000 0.495 -0.741 -26.026 -26.273 HBUILD: HD21,HD22, , constructed (spin) for donor BET1 3 ASN ND2 . MAKINB: mode 5 found 4 exclusions, 2 interactions(1-4) and 2 GB exclusions HBONDS: allocating space for 44 h-bond interactions. HBONDS: 6 distance exclusions and 0 angle exclusions HBONDS: 670 fixed h-bonds, currently 17 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 1.000 -0.010 -36.895 -35.904 10.0 0.000 0.933 0.044 -37.997 -37.020 20.0 0.000 0.750 -0.003 -39.303 -38.556 30.0 0.000 0.500 -0.147 -40.764 -40.412 40.0 0.000 0.250 -0.331 -42.290 -42.371 50.0 0.000 0.067 -0.482 -43.752 -44.167 60.0 0.000 0.000 -0.562 -45.006 -45.568 70.0 0.000 0.067 -0.578 -45.905 -46.416 80.0 0.000 0.250 -0.555 -46.321 -46.627 90.0 0.000 0.500 -0.518 -46.192 -46.210 100.0 0.000 0.750 -0.479 -45.535 -45.264 110.0 0.000 0.933 -0.441 -44.440 -43.948 120.0 0.000 1.000 -0.408 -43.036 -42.443 130.0 0.000 0.933 -0.379 -41.467 -40.913 140.0 0.000 0.750 -0.354 -39.866 -39.470 150.0 0.000 0.500 -0.334 -38.336 -38.170 160.0 0.000 0.250 -0.315 -36.959 -37.023 170.0 0.000 0.067 -0.295 -35.784 -36.012 180.0 0.000 0.000 -0.271 -34.849 -35.120 190.0 0.000 0.067 -0.241 -34.167 -34.341 200.0 0.000 0.250 -0.204 -33.741 -33.695 210.0 -0.004 0.500 -0.167 -33.553 -33.224 220.0 -0.064 0.750 -0.140 -33.562 -33.016 230.0 -0.146 0.933 -0.138 -33.716 -33.067 240.0 -0.217 1.000 -0.169 -33.949 -33.335 250.0 -0.243 0.933 -0.228 -34.194 -33.732 260.0 -0.205 0.750 -0.303 -34.389 -34.147 270.0 -0.129 0.500 -0.378 -34.499 -34.505 280.0 -0.059 0.250 -0.440 -34.521 -34.769 290.0 -0.019 0.067 -0.483 -34.493 -34.928 300.0 -0.006 0.000 -0.502 -34.466 -34.973 310.0 -0.002 0.067 -0.493 -34.496 -34.924 320.0 -0.001 0.250 -0.450 -34.630 -34.831 330.0 0.000 0.500 -0.371 -34.906 -34.777 340.0 0.000 0.750 -0.257 -35.359 -34.867 350.0 0.000 0.933 -0.126 -36.015 -35.208 HBUILD: HG1 , , , constructed (spin) for donor BET1 4 THR OG1 . MAKINB: mode 5 found 15 exclusions, 6 interactions(1-4) and 9 GB exclusions HBONDS: allocating space for 25 h-bond interactions. HBONDS: ran out of space. Starting over. HBONDS: allocating space for 333 h-bond interactions. HBONDS: 36 distance exclusions and 0 angle exclusions HBONDS: 621 fixed h-bonds, currently 36 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 3.600 -0.346 -18.415 -15.161 10.0 0.000 3.359 -0.365 -18.546 -15.551 20.0 -0.009 2.700 -0.417 -18.640 -16.365 30.0 -0.029 1.800 -0.483 -18.683 -17.395 40.0 -0.050 0.900 -0.544 -18.669 -18.362 50.0 -0.069 0.241 -0.586 -18.602 -19.016 60.0 -0.077 0.000 -0.603 -18.498 -19.178 70.0 -0.070 0.241 -0.592 -18.379 -18.801 80.0 -0.053 0.900 -0.555 -18.272 -17.979 90.0 -0.032 1.800 -0.495 -18.216 -16.943 100.0 -0.016 2.700 -0.426 -18.226 -15.968 110.0 -0.003 3.359 -0.370 -18.294 -15.308 HBUILD: HT1 ,HT2 ,HT3 , constructed (spin) for donor BET2 1 SER N . MAKINB: mode 5 found 3 exclusions, 1 interactions(1-4) and 2 GB exclusions HBONDS: allocating space for 49 h-bond interactions. HBONDS: 11 distance exclusions and 0 angle exclusions HBONDS: 670 fixed h-bonds, currently 12 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 1.000 2.527 20.116 23.642 10.0 -0.001 0.933 1.480 19.567 21.980 20.0 -0.003 0.750 0.751 18.790 20.287 30.0 -0.004 0.500 0.288 17.853 18.637 40.0 -0.003 0.250 0.013 16.817 17.077 50.0 -0.001 0.067 -0.138 15.712 15.640 60.0 0.000 0.000 -0.211 14.564 14.353 70.0 0.000 0.067 -0.237 13.402 13.232 80.0 0.000 0.250 -0.239 12.244 12.256 90.0 0.000 0.500 -0.230 11.107 11.377 100.0 0.000 0.750 -0.219 10.003 10.534 110.0 0.000 0.933 -0.208 8.944 9.669 120.0 0.000 1.000 -0.202 7.946 8.744 130.0 0.000 0.933 -0.200 7.028 7.761 140.0 0.000 0.750 -0.203 6.215 6.762 150.0 0.000 0.500 -0.212 5.537 5.825 160.0 0.000 0.250 -0.228 5.028 5.051 170.0 0.000 0.067 -0.251 4.727 4.543 180.0 0.000 0.000 -0.282 4.664 4.382 190.0 0.000 0.067 -0.319 4.853 4.601 200.0 0.000 0.250 -0.361 5.305 5.194 210.0 0.000 0.500 -0.404 6.023 6.119 220.0 0.000 0.750 -0.440 6.981 7.291 230.0 0.000 0.933 -0.463 8.131 8.601 240.0 0.000 1.000 -0.473 9.420 9.946 250.0 0.000 0.933 -0.469 10.784 11.247 260.0 0.000 0.750 -0.443 12.168 12.475 270.0 0.000 0.500 -0.358 13.532 13.673 280.0 0.000 0.250 -0.139 14.853 14.964 290.0 0.000 0.067 0.346 16.121 16.533 300.0 0.000 0.000 1.244 17.313 18.558 310.0 0.000 0.067 2.576 18.393 21.035 320.0 0.000 0.250 4.011 19.300 23.561 330.0 0.000 0.500 4.897 19.966 25.363 340.0 0.000 0.750 4.757 20.335 25.842 350.0 0.000 0.933 3.768 20.383 25.084 HBUILD: HG , , , constructed (spin) for donor BET2 1 SER OG . MAKINB: mode 5 found 4 exclusions, 2 interactions(1-4) and 2 GB exclusions HBONDS: allocating space for 18 h-bond interactions. HBONDS: 7 distance exclusions and 0 angle exclusions HBONDS: 670 fixed h-bonds, currently 16 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 1.000 -0.545 16.559 17.013 10.0 0.000 0.933 -0.583 18.212 18.562 20.0 0.000 0.750 -0.574 20.137 20.313 30.0 -0.004 0.500 -0.358 22.346 22.484 40.0 -0.020 0.250 0.602 24.862 25.693 50.0 -0.037 0.067 4.329 27.712 32.071 60.0 -0.040 0.000 18.760 30.882 49.603 70.0 -0.033 0.067 70.867 34.212 105.113 80.0 -0.019 0.250 211.517 37.235 248.983 90.0 -0.006 0.500 397.379 39.134 437.008 100.0 0.000 0.750 388.597 39.160 428.507 110.0 0.000 0.933 198.740 37.325 236.998 120.0 0.000 1.000 64.365 34.385 99.750 130.0 0.000 0.933 16.366 31.145 48.444 140.0 0.000 0.750 3.542 28.064 32.355 150.0 0.000 0.500 0.420 25.309 26.229 160.0 0.000 0.250 -0.307 22.904 22.847 170.0 0.000 0.067 -0.443 20.829 20.454 180.0 0.000 0.000 -0.427 19.058 18.631 190.0 0.000 0.067 -0.373 17.550 17.244 200.0 0.000 0.250 -0.309 16.267 16.208 210.0 0.000 0.500 -0.244 15.181 15.438 220.0 0.000 0.750 -0.186 14.268 14.831 230.0 0.000 0.933 -0.147 13.509 14.294 240.0 0.000 1.000 -0.135 12.893 13.758 250.0 0.000 0.933 -0.152 12.411 13.191 260.0 0.000 0.750 -0.192 12.058 12.615 270.0 0.000 0.500 -0.244 11.828 12.085 280.0 0.000 0.250 -0.296 11.720 11.674 290.0 0.000 0.067 -0.342 11.732 11.457 300.0 0.000 0.000 -0.380 11.869 11.489 310.0 0.000 0.067 -0.411 12.146 11.803 320.0 0.000 0.250 -0.435 12.589 12.404 330.0 0.000 0.500 -0.457 13.224 13.267 340.0 0.000 0.750 -0.479 14.078 14.349 350.0 0.000 0.933 -0.508 15.181 15.607 HBUILD: HG1 , , , constructed (spin) for donor BET2 3 THR OG1 . MAKINB: mode 5 found 9 exclusions, 4 interactions(1-4) and 5 GB exclusions HBONDS: allocating space for 23 h-bond interactions. HBONDS: ran out of space. Starting over. HBONDS: allocating space for 333 h-bond interactions. HBONDS: 18 distance exclusions and 0 angle exclusions HBONDS: 645 fixed h-bonds, currently 30 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 0.000 -0.490 -36.615 -37.105 10.0 0.000 0.989 -0.519 -36.187 -35.717 20.0 0.000 3.837 -0.573 -35.902 -32.638 30.0 0.000 8.200 -0.633 -35.789 -28.222 40.0 0.000 13.552 -0.680 -35.861 -22.989 50.0 0.000 19.248 -0.706 -36.114 -17.572 60.0 0.000 24.600 -0.711 -36.524 -12.635 70.0 0.000 28.963 -0.702 -37.051 -8.790 80.0 0.000 31.811 -0.688 -37.635 -6.512 90.0 -0.001 32.800 -0.672 -38.207 -6.079 100.0 -0.014 31.811 -0.658 -38.690 -7.551 110.0 -0.038 28.963 -0.646 -39.017 -10.738 120.0 -0.044 24.600 -0.634 -39.144 -15.222 130.0 -0.025 19.248 -0.619 -39.048 -20.445 140.0 -0.005 13.552 -0.596 -38.751 -25.800 150.0 0.000 8.200 -0.563 -38.293 -30.656 160.0 0.000 3.837 -0.524 -37.736 -34.424 170.0 0.000 0.989 -0.494 -37.154 -36.659 HBUILD: HH11,HH12, , constructed (spin) for donor BET2 6 ARG NH1 . MAKINB: mode 5 found 9 exclusions, 4 interactions(1-4) and 5 GB exclusions HBONDS: allocating space for 42 h-bond interactions. HBONDS: 20 distance exclusions and 0 angle exclusions HBONDS: 645 fixed h-bonds, currently 28 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 0.000 -0.528 -34.795 -35.323 10.0 0.000 0.989 -0.528 -35.345 -34.884 20.0 0.000 3.837 -0.525 -35.843 -32.531 30.0 -0.001 8.200 -0.519 -36.251 -28.570 40.0 -0.014 13.552 -0.511 -36.528 -23.502 50.0 -0.050 19.248 -0.503 -36.633 -17.938 60.0 -0.076 24.600 -0.495 -36.534 -12.505 70.0 -0.088 28.963 -0.489 -36.222 -7.836 80.0 -0.081 31.811 -0.483 -35.725 -4.479 90.0 -0.057 32.800 -0.480 -35.106 -2.843 100.0 -0.018 31.811 -0.479 -34.452 -3.139 110.0 -0.001 28.963 -0.481 -33.865 -5.383 120.0 0.000 24.600 -0.485 -33.426 -9.311 130.0 0.000 19.248 -0.493 -33.192 -14.436 140.0 0.000 13.552 -0.502 -33.182 -20.132 150.0 0.000 8.200 -0.511 -33.385 -25.696 160.0 0.000 3.837 -0.519 -33.760 -30.442 170.0 0.000 0.989 -0.525 -34.248 -33.784 HBUILD: HH21,HH22, , constructed (spin) for donor BET2 6 ARG NH2 . X-PLOR>! X-PLOR>! TEST HBUILD with waters X-PLOR>! X-PLOR>hbuild HBUILD> selection=( segid TIP3 and hydrogen ) SELRPN: 10 atoms have been selected out of 158 HBUILD> acceptors=( name O* ) !! acceptor definition SELRPN: 29 atoms have been selected out of 158 HBUILD> print=true phistp=10.0 cutwat=5.7 HBUILD>end HBUILD: dihedral PHI STePs for spin = 10.0000 HBUILD: cutoff during water acceptor search = 5.7000 MAKINB: mode 5 found 3 exclusions, 0 interactions(1-4) and 3 GB exclusions HBONDS: allocating space for 39 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 693 fixed h-bonds, currently 0 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 0.000 -0.155 -50.564 -50.719 10.0 0.000 0.000 -0.143 -49.544 -49.687 20.0 0.000 0.000 -0.132 -47.747 -47.878 30.0 0.000 0.000 -0.121 -45.370 -45.491 40.0 0.000 0.000 -0.112 -42.647 -42.759 50.0 0.000 0.000 -0.106 -39.770 -39.876 60.0 0.000 0.000 -0.103 -36.895 -36.998 70.0 0.000 0.000 -0.104 -34.113 -34.217 80.0 0.000 0.000 -0.108 -31.486 -31.593 90.0 0.000 0.000 -0.115 -29.053 -29.168 100.0 0.000 0.000 -0.125 -26.830 -26.955 110.0 0.000 0.000 -0.140 -24.839 -24.978 120.0 0.000 0.000 -0.158 -23.169 -23.327 130.0 0.000 0.000 -0.179 -21.941 -22.120 140.0 0.000 0.000 -0.202 -21.275 -21.477 150.0 0.000 0.000 -0.224 -21.245 -21.469 160.0 0.000 0.000 -0.243 -21.842 -22.085 170.0 0.000 0.000 -0.256 -22.980 -23.236 180.0 0.000 0.000 -0.264 -24.530 -24.794 190.0 0.000 0.000 -0.268 -26.403 -26.671 200.0 0.000 0.000 -0.269 -28.554 -28.824 210.0 0.000 0.000 -0.270 -30.957 -31.226 220.0 0.000 0.000 -0.272 -33.535 -33.807 230.0 0.000 0.000 -0.278 -36.147 -36.424 240.0 0.000 0.000 -0.286 -38.601 -38.888 250.0 0.000 0.000 -0.295 -40.730 -41.025 260.0 0.000 0.000 -0.300 -42.429 -42.729 270.0 0.000 0.000 -0.299 -43.693 -43.992 280.0 0.000 0.000 -0.290 -44.600 -44.889 290.0 0.000 0.000 -0.275 -45.306 -45.581 300.0 0.000 0.000 -0.257 -46.000 -46.256 310.0 0.000 0.000 -0.236 -46.862 -47.098 320.0 0.000 0.000 -0.215 -47.957 -48.172 330.0 0.000 0.000 -0.196 -49.150 -49.346 340.0 0.000 0.000 -0.180 -50.179 -50.359 350.0 0.000 0.000 -0.167 -50.737 -50.903 HBUILD:H1 ,H2 , , constructed for water TIP3 1 TIP3 HBUILD: Minimum distance between water and solute is 2.26025 A. MAKINB: mode 5 found 2 exclusions, 0 interactions(1-4) and 2 GB exclusions HBONDS: allocating space for 333 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 693 fixed h-bonds, currently 0 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 0.000 -0.019 8.880 8.861 10.0 0.000 0.000 -0.021 9.580 9.559 20.0 0.000 0.000 -0.024 10.461 10.437 30.0 0.000 0.000 -0.027 11.533 11.506 40.0 0.000 0.000 -0.032 12.798 12.766 50.0 0.000 0.000 -0.037 14.254 14.217 60.0 0.000 0.000 -0.044 15.887 15.843 70.0 0.000 0.000 -0.052 17.659 17.607 80.0 0.000 0.000 -0.061 19.512 19.451 90.0 0.000 0.000 -0.070 21.359 21.288 100.0 0.000 0.000 -0.080 23.079 22.999 110.0 0.000 0.000 -0.088 24.523 24.436 120.0 0.000 0.000 -0.093 25.499 25.406 130.0 0.000 0.000 -0.094 25.865 25.771 140.0 0.000 0.000 -0.091 25.563 25.472 150.0 0.000 0.000 -0.085 24.640 24.555 160.0 0.000 0.000 -0.076 23.214 23.138 170.0 0.000 0.000 -0.067 21.452 21.385 180.0 0.000 0.000 -0.057 19.539 19.482 190.0 0.000 0.000 -0.049 17.635 17.586 200.0 0.000 0.000 -0.042 15.849 15.807 210.0 0.000 0.000 -0.036 14.242 14.207 220.0 0.000 0.000 -0.031 12.838 12.807 230.0 0.000 0.000 -0.027 11.630 11.604 240.0 0.000 0.000 -0.024 10.601 10.577 250.0 0.000 0.000 -0.021 9.728 9.707 260.0 0.000 0.000 -0.019 9.027 9.008 270.0 0.000 0.000 -0.017 8.492 8.474 280.0 0.000 0.000 -0.016 8.102 8.086 290.0 0.000 0.000 -0.015 7.825 7.810 300.0 0.000 0.000 -0.015 7.649 7.634 310.0 0.000 0.000 -0.014 7.571 7.556 320.0 0.000 0.000 -0.015 7.593 7.579 330.0 0.000 0.000 -0.015 7.720 7.705 340.0 0.000 0.000 -0.016 7.965 7.949 350.0 0.000 0.000 -0.017 8.347 8.329 HBUILD:H1 , Spin:H2 , , constructed for water TIP3 5 TIP3 OH2 . HBUILD: Minimum distance between water and solute is 2.50544 A. MAKINB: mode 5 found 3 exclusions, 0 interactions(1-4) and 3 GB exclusions HBONDS: allocating space for 333 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 693 fixed h-bonds, currently 0 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 0.000 -0.172 -2.142 -2.314 10.0 0.000 0.000 -0.163 -3.606 -3.769 20.0 0.000 0.000 -0.152 -4.653 -4.805 30.0 0.000 0.000 -0.140 -5.174 -5.314 40.0 0.000 0.000 -0.129 -5.156 -5.285 50.0 0.000 0.000 -0.120 -4.641 -4.760 60.0 0.000 0.000 -0.112 -3.690 -3.803 70.0 0.000 0.000 -0.107 -2.383 -2.489 80.0 0.000 0.000 -0.103 -0.787 -0.890 90.0 0.000 0.000 -0.100 1.020 0.920 100.0 0.000 0.000 -0.099 2.954 2.856 110.0 0.000 0.000 -0.099 4.954 4.855 120.0 0.000 0.000 -0.100 7.022 6.921 130.0 0.000 0.000 -0.104 9.138 9.034 140.0 0.000 0.000 -0.110 11.290 11.180 150.0 0.000 0.000 -0.117 13.451 13.334 160.0 0.000 0.000 -0.127 15.561 15.434 170.0 0.000 0.000 -0.137 17.494 17.357 180.0 0.000 0.000 -0.147 19.049 18.901 190.0 0.000 0.000 -0.156 19.980 19.824 200.0 0.000 0.000 -0.163 20.098 19.935 210.0 0.000 0.000 -0.169 19.409 19.239 220.0 0.000 0.000 -0.176 18.100 17.924 230.0 0.000 0.000 -0.183 16.427 16.244 240.0 0.000 0.000 -0.189 14.577 14.388 250.0 0.000 0.000 -0.194 12.726 12.532 260.0 0.000 0.000 -0.196 11.073 10.876 270.0 0.000 0.000 -0.196 9.762 9.566 280.0 0.000 0.000 -0.194 8.804 8.610 290.0 0.000 0.000 -0.190 8.023 7.833 300.0 0.000 0.000 -0.187 7.145 6.958 310.0 0.000 0.000 -0.183 5.988 5.804 320.0 0.000 0.000 -0.181 4.551 4.370 330.0 0.000 0.000 -0.180 2.953 2.773 340.0 0.000 0.000 -0.179 1.275 1.096 350.0 0.000 0.000 -0.177 -0.450 -0.627 HBUILD:H1 ,H2 , , constructed for water TIP3 4 TIP3 HBUILD: Minimum distance between water and solute is 2.54303 A. MAKINB: mode 5 found 3 exclusions, 0 interactions(1-4) and 3 GB exclusions HBONDS: allocating space for 333 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 693 fixed h-bonds, currently 0 h-bonds present rel. PHI HBONDS DIHEDRALS VDW ELEC ENERGY 0.0 0.000 0.000 -0.192 -32.756 -32.948 10.0 0.000 0.000 -0.177 -31.318 -31.495 20.0 0.000 0.000 -0.155 -29.244 -29.399 30.0 0.000 0.000 -0.131 -26.709 -26.840 40.0 0.000 0.000 -0.108 -23.921 -24.029 50.0 0.000 0.000 -0.089 -21.062 -21.151 60.0 0.000 0.000 -0.075 -18.267 -18.342 70.0 0.000 0.000 -0.065 -15.626 -15.692 80.0 0.000 0.000 -0.060 -13.196 -13.256 90.0 0.000 0.000 -0.057 -10.988 -11.045 100.0 0.000 0.000 -0.058 -9.035 -9.093 110.0 0.000 0.000 -0.060 -7.375 -7.435 120.0 0.000 0.000 -0.064 -6.053 -6.116 130.0 0.000 0.000 -0.069 -5.122 -5.191 140.0 0.000 0.000 -0.075 -4.634 -4.709 150.0 0.000 0.000 -0.082 -4.635 -4.717 160.0 0.000 0.000 -0.090 -5.174 -5.264 170.0 0.000 0.000 -0.099 -6.272 -6.371 180.0 0.000 0.000 -0.110 -7.895 -8.005 190.0 0.000 0.000 -0.123 -9.963 -10.086 200.0 0.000 0.000 -0.140 -12.364 -12.504 210.0 0.000 0.000 -0.160 -14.962 -15.123 220.0 0.000 0.000 -0.183 -17.594 -17.777 230.0 0.000 0.000 -0.205 -20.101 -20.306 240.0 0.000 0.000 -0.223 -22.341 -22.564 250.0 0.000 0.000 -0.232 -24.206 -24.438 260.0 0.000 0.000 -0.231 -25.668 -25.900 270.0 0.000 0.000 -0.221 -26.815 -27.036 280.0 0.000 0.000 -0.207 -27.786 -27.993 290.0 0.000 0.000 -0.192 -28.731 -28.923 300.0 0.000 0.000 -0.183 -29.748 -29.931 310.0 0.000 0.000 -0.180 -30.846 -31.026 320.0 0.000 0.000 -0.183 -31.939 -32.123 330.0 0.000 0.000 -0.190 -32.875 -33.066 340.0 0.000 0.000 -0.197 -33.451 -33.648 350.0 0.000 0.000 -0.199 -33.457 -33.656 HBUILD:H1 ,H2 , , constructed for water TIP3 2 TIP3 HBUILD: Minimum distance between water and solute is 3.20819 A. HBUILD:H1 ,H2 , , placed for water TIP3 3 TIP3 OH2 . HBUILD: Minimum distance between water and solute is 14.06475 A. X-PLOR>! X-PLOR>coor rms sele=( not ( hydrogen ) ) end SELRPN: 119 atoms have been selected out of 158 COOR: using atom subset. COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.000000, square sum= 0.0000, denominator= 119.0000 X-PLOR>! X-PLOR>write coor sele=( hydrogen ) end SELRPN: 39 atoms have been selected out of 158 CWRITE: using atom subset. REMARK FILENAME="OUTPUT" REMARK coordinates obtained from Greg Petsko REMARK neutron diffraction structure of ribonuclease REMARK DATE:04-Jun-04 10:27:31 created by user: [unknown] ATOM 1 HT1 PRO 1 26.447 6.582 6.766 1.00 0.00 BET1 ATOM 2 HT2 PRO 1 27.193 7.938 7.464 1.00 0.00 BET1 ATOM 11 H VAL 2 28.839 8.486 8.077 1.00 0.00 BET1 ATOM 19 H ASN 3 29.095 9.937 12.078 1.00 0.00 BET1 ATOM 25 HD21 ASN 3 25.252 13.333 12.747 1.00 0.00 BET1 ATOM 26 HD22 ASN 3 25.473 14.917 12.121 1.00 0.00 BET1 ATOM 30 H THR 4 29.426 14.218 12.387 1.00 0.00 BET1 ATOM 34 HG1 THR 4 31.862 13.818 13.066 1.00 0.00 BET1 ATOM 39 H PHE 5 28.603 14.722 16.636 1.00 0.00 BET1 ATOM 51 H VAL 6 27.468 18.963 16.948 1.00 0.00 BET1 ATOM 59 H HIS 7 28.950 19.514 21.088 1.00 0.00 BET1 ATOM 65 HD1 HIS 7 24.835 18.120 22.836 1.00 0.00 BET1 ATOM 68 HE2 HIS 7 26.932 14.838 21.813 1.00 0.00 BET1 ATOM 72 HT1 SER 1 32.069 20.286 23.112 1.00 0.00 BET2 ATOM 73 HT2 SER 1 33.445 19.335 22.822 1.00 0.00 BET2 ATOM 75 HT3 SER 1 33.124 19.908 24.388 1.00 0.00 BET2 ATOM 79 HG SER 1 29.305 17.576 25.341 1.00 0.00 BET2 ATOM 83 H ILE 2 32.235 16.105 22.530 1.00 0.00 BET2 ATOM 92 H THR 3 29.618 14.945 19.314 1.00 0.00 BET2 ATOM 96 HG1 THR 3 27.878 12.907 22.238 1.00 0.00 BET2 ATOM 101 H ASP 4 30.631 10.976 19.285 1.00 0.00 BET2 ATOM 110 H CYS 5 29.358 10.127 15.169 1.00 0.00 BET2 ATOM 117 H ARG 6 28.573 6.059 15.396 1.00 0.00 BET2 ATOM 123 HE ARG 6 32.855 4.992 14.746 1.00 0.00 BET2 ATOM 126 HH11 ARG 6 33.985 6.946 11.963 1.00 0.00 BET2 ATOM 127 HH12 ARG 6 35.032 7.884 12.975 1.00 0.00 BET2 ATOM 129 HH21 ARG 6 34.321 6.153 15.934 1.00 0.00 BET2 ATOM 130 HH22 ARG 6 35.228 7.435 15.203 1.00 0.00 BET2 ATOM 134 H GLU 7 28.724 4.560 11.336 1.00 0.00 BET2 ATOM 145 H1 TIP3 1 31.613 14.025 11.152 1.00 0.00 TIP3 ATOM 146 H2 TIP3 1 31.068 14.489 9.818 1.00 0.00 TIP3 ATOM 148 H1 TIP3 2 28.261 21.513 25.402 1.00 0.00 TIP3 ATOM 149 H2 TIP3 2 27.727 21.282 26.799 1.00 0.00 TIP3 ATOM 151 H1 TIP3 3 12.857 5.760 14.215 1.00 0.00 TIP3 ATOM 152 H2 TIP3 3 12.857 4.563 13.288 1.00 0.00 TIP3 ATOM 154 H1 TIP3 4 33.301 12.570 12.522 1.00 0.00 TIP3 ATOM 155 H2 TIP3 4 34.138 11.838 11.495 1.00 0.00 TIP3 ATOM 157 H1 TIP3 5 31.860 3.818 16.495 1.00 0.00 TIP3 ATOM 158 H2 TIP3 5 32.549 3.290 17.735 1.00 0.00 TIP3 END X-PLOR>! X-PLOR>stop HEAP: maximum use= 904569 current use= 873507 X-PLOR: total CPU time= 0.2000 s X-PLOR: entry time at 10:27:31 04-Jun-04 X-PLOR: exit time at 10:27:31 04-Jun-04