MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:38:51 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v16}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v16}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v16}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 openf___224_> Open ${MODINSTALL9v16}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v16}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v16}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v16}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 402709 393.271 0.384 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 404309 394.833 0.386 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 408289 398.720 0.389 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 410289 400.673 0.391 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 413289 403.603 0.394 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 417789 407.997 0.398 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 423361 413.438 0.404 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 426161 416.173 0.406 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 430361 420.274 0.410 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 436661 426.427 0.416 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 439433 429.134 0.419 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 440833 430.501 0.420 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open $(LIB)/atmcls-melo.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 441259 430.917 0.421 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 441323 430.979 0.421 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 441387 431.042 0.421 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 441515 431.167 0.421 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 441707 431.354 0.421 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 441963 431.604 0.421 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 442347 431.979 0.422 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 442923 432.542 0.422 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 442973 432.591 0.422 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 443031 432.647 0.423 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 443927 433.522 0.423 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 445271 434.835 0.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 445337 434.899 0.425 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 447321 436.837 0.427 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 447477 436.989 0.427 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 450485 439.927 0.430 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 450779 440.214 0.430 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 451283 440.706 0.430 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 452279 441.679 0.431 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 456759 446.054 0.436 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 458793 448.040 0.438 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 463245 452.388 0.442 openf___224_> Open $(LIB)/melo1-dist.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 463641 452.774 0.442 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 464437 453.552 0.443 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 465233 454.329 0.444 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 466421 455.489 0.445 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 466821 455.880 0.445 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 467421 456.466 0.446 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 468321 457.345 0.447 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 469669 458.661 0.448 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 471693 460.638 0.450 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 471893 460.833 0.450 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 474929 463.798 0.453 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 475229 464.091 0.453 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 479781 468.536 0.458 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 480229 468.974 0.458 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 487057 475.642 0.464 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 487729 476.298 0.465 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 497973 486.302 0.475 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 498981 487.286 0.476 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 499581 487.872 0.476 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 499981 488.263 0.477 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 515345 503.267 0.491 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 516857 504.743 0.493 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 517757 505.622 0.494 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 518357 506.208 0.494 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 541405 528.716 0.516 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 543673 530.931 0.518 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 545017 532.243 0.520 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 545917 533.122 0.521 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 580489 566.884 0.554 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 583893 570.208 0.557 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 585909 572.177 0.559 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 587257 573.493 0.560 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 639113 624.134 0.610 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 644217 629.118 0.614 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 647241 632.071 0.617 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 649265 634.048 0.619 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 727049 710.009 0.693 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 734705 717.485 0.701 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 739241 721.915 0.705 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 742277 724.880 0.708 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 858953 838.821 0.819 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 0 0 0 0 820 openf___224_> Open 1fdx.B99990001.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 860619 840.448 0.821 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 860695 840.522 0.821 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 860866 840.689 0.821 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 861716 841.520 0.822 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 862974 842.748 0.823 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 864878 844.607 0.825 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 864918 844.646 0.825 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 865008 844.734 0.825 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 867864 847.523 0.828 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 867924 847.582 0.828 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 868059 847.714 0.828 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 872343 851.897 0.832 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 872431 851.983 0.832 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 872629 852.177 0.832 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 906261 885.021 0.864 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 908359 887.069 0.866 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 937955 915.972 0.895 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 938605 916.606 0.895 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 968201 945.509 0.923 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 973625 950.806 0.929 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 0 0 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 989861 966.661 0.944 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 518 628 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1007837 984.216 0.961 patch_______> segment topology patched using RTF: 54 ; ASP ; CTER segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 openf___224_> Open 1fdx.B99990001.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1018790 994.912 0.972 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1018866 994.986 0.972 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1019037 995.153 0.972 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1019887 995.983 0.973 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1021145 997.212 0.974 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1023049 999.071 0.976 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1023089 999.110 0.976 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1023179 999.198 0.976 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1026035 1001.987 0.979 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1026095 1002.046 0.979 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1026230 1002.178 0.979 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1030514 1006.361 0.983 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1030602 1006.447 0.983 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1030800 1006.641 0.983 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1064432 1039.484 1.015 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 # ALGNMT CODE 1 1fdx 2 1fdx transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 373 0 77 atoms selected for loop refinement make_re_417_> Restraint type to be calculated: bond Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1114305 1088.188 1.063 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 80 0 0 0 Total number of restraints before, now : 0 80 make_re_422_> Number of previous, current restraints : 0 80 make_re_423_> Number of previous, current selected restraints: 0 80 make_re_417_> Restraint type to be calculated: angle r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 112 0 0 Total number of restraints before, now : 80 192 make_re_422_> Number of previous, current restraints : 80 192 make_re_423_> Number of previous, current selected restraints: 80 192 make_re_417_> Restraint type to be calculated: improper r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 0 36 Total number of restraints before, now : 192 228 make_re_422_> Number of previous, current restraints : 192 228 make_re_423_> Number of previous, current selected restraints: 192 228 make_re_417_> Restraint type to be calculated: dihedral Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1122497 1096.188 1.070 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 0 0 138 0 Total number of restraints before, now : 228 366 make_re_422_> Number of previous, current restraints : 228 366 make_re_423_> Number of previous, current selected restraints: 228 366 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1122497 1096.188 1.070 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 366 378 make_re_423_> Number of previous, current selected restraints: 366 378 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1122513 1096.204 1.071 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 12 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 378 389 make_re_423_> Number of previous, current selected restraints: 378 377 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1122513 1096.204 1.071 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 389 398 make_re_423_> Number of previous, current selected restraints: 377 386 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1122513 1096.204 1.071 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 398 405 make_re_423_> Number of previous, current selected restraints: 386 393 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1122513 1096.204 1.071 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 405 407 make_re_423_> Number of previous, current selected restraints: 393 395 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1122513 1096.204 1.071 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 1fdx getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 407 407 make_re_423_> Number of previous, current selected restraints: 395 395 pick_re_612_> Number of MODEL atoms, selected restraints; 77 407 rmdupl__427_> 68 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 407 339 openf___224_> Open 1fdx.lrsr preppdf_457W> Both soft sphere and statistical potential terms selected. Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1229901 1201.075 1.173 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1531457 1495.563 1.461 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1540409 1504.306 1.469 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1558313 1521.790 1.486 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2322 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 194.0620 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 80 0 0 0.007 0.007 1.1290 1.000 2 Bond angle potential : 112 0 2 2.875 2.875 19.061 1.000 3 Stereochemical cosine torsion poten: 70 0 2 45.200 45.200 22.431 1.000 4 Stereochemical improper torsion pot: 36 0 0 1.099 1.099 0.92415 1.000 5 Soft-sphere overlap restraints : 2322 0 0 0.001 0.001 0.28444 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 11 0 2 7.947 7.947 8.1989 1.000 14 Sidechain Chi_1 dihedral restraints: 9 0 0 73.452 73.452 2.1946 1.000 15 Sidechain Chi_2 dihedral restraints: 7 0 0 20.327 20.327 -0.17386E-01 1.000 16 Sidechain Chi_3 dihedral restraints: 2 0 0 10.516 10.516 0.50948 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 12 9 2 25.602 152.488 10.625 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 2322 0 18 1.827 1.827 128.72 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 300 18C 19P C N 124 126 -67.52 -58.70 8.82 1.13 -64.50 177.78 13.43 1 19P 19P N CA 126 127 -30.55 -30.50 147.20 2 301 19P 20V C N 131 133 -74.18 -62.40 17.31 1.97 -125.40 -179.55 7.52 2 20V 20V N CA 133 134 -29.73 -42.40 143.30 3 302 20V 21N C N 138 140 68.45 55.90 16.10 1.08 -63.20 149.35 24.54 3 21N 21N N CA 140 141 29.43 39.50 -41.10 4 303 21N 22I C N 146 148 -71.11 -63.40 10.44 1.61 -120.60 174.05 8.13 4 22I 22I N CA 148 149 -36.57 -43.60 130.30 5 304 22I 23I C N 154 156 -63.69 -63.40 4.93 0.82 -120.60 -172.34 8.65 5 23I 23I N CA 156 157 -48.53 -43.60 130.30 6 305 23I 24Q C N 162 164 -14.29 -73.00 59.68 4.05 -63.80 177.31 28.72 6 24Q 24Q N CA 164 165 129.96 140.70 -40.30 7 306 24Q 25G C N 171 173 157.62 -167.20 40.83 1.33 82.20 163.78 11.37 7 25G 25G N CA 173 174 153.88 174.60 8.50 8 309 27I 28Y C N 189 191 -70.29 -98.40 28.48 1.13 -63.50 176.50 27.67 8 28Y 28Y N CA 191 192 132.97 128.40 -43.40 9 310 28Y 29A C N 201 203 -130.91 -134.00 4.92 0.30 -62.50 -178.35 33.44 9 29A 29A N CA 203 204 150.83 147.00 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 3 5 21 32 40 42 54 44 49 73 << end of ENERGY. openf___224_> Open 1fdx.IL00000001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1558333 1521.810 1.486 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 373 77 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1414 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 73.0276 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 80 0 0 0.010 0.010 2.3046 1.000 2 Bond angle potential : 112 0 2 3.193 3.193 22.130 1.000 3 Stereochemical cosine torsion poten: 70 0 3 46.750 46.750 24.364 1.000 4 Stereochemical improper torsion pot: 36 0 0 2.423 2.423 3.9268 1.000 5 Soft-sphere overlap restraints : 1414 0 0 0.000 0.000 0.15457E-01 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 11 0 0 3.735 3.735 1.8108 1.000 14 Sidechain Chi_1 dihedral restraints: 9 0 0 76.168 76.168 3.7445 1.000 15 Sidechain Chi_2 dihedral restraints: 7 0 0 47.042 47.042 3.2282 1.000 16 Sidechain Chi_3 dihedral restraints: 2 0 0 127.217 127.217 0.69440 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 12 8 4 35.501 155.172 16.786 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 1414 0 3 1.854 1.854 -5.9771 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 300 18C 19P C N 124 126 -66.11 -58.70 18.01 1.06 -64.50 161.30 12.12 1 19P 19P N CA 126 127 -14.09 -30.50 147.20 2 302 20V 21N C N 138 140 47.19 55.90 47.39 2.71 -63.20 168.41 26.91 2 21N 21N N CA 140 141 86.08 39.50 -41.10 3 303 21N 22I C N 146 148 -73.05 -63.40 9.71 1.70 -120.60 179.19 8.48 3 22I 22I N CA 148 149 -42.46 -43.60 130.30 4 305 23I 24Q C N 162 164 -86.54 -73.00 27.25 1.57 -63.80 157.00 24.30 4 24Q 24Q N CA 164 165 164.35 140.70 -40.30 5 307 25G 26S C N 175 177 -65.24 -72.40 41.26 2.19 -64.10 146.77 10.57 5 26S 26S N CA 177 178 111.76 152.40 -35.00 6 308 26S 27I C N 181 183 -70.79 -63.40 7.43 1.35 -120.60 -178.37 8.54 6 27I 27I N CA 183 184 -44.36 -43.60 130.30 7 309 27I 28Y C N 189 191 -91.65 -98.40 11.67 1.08 -63.50 164.71 24.76 7 28Y 28Y N CA 191 192 118.88 128.40 -43.40 8 310 28Y 29A C N 201 203 141.70 -134.00 84.39 2.65 -62.50 -130.67 45.59 8 29A 29A N CA 203 204 150.83 147.00 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 2 5 19 26 32 31 56 46 42 63 << end of ENERGY. iupac_m_483_> CD1/2 CE1/2 swapped: 106.3981 28 28 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. openf___224_> Open 1fdx.BL00200001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open ${LIB}/atmcls-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1558725 1522.192 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1558789 1522.255 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1558847 1522.312 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1558911 1522.374 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1558977 1522.438 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1559041 1522.501 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1559197 1522.653 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1559325 1522.778 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1559619 1523.065 1.487 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1559811 1523.253 1.488 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1560315 1523.745 1.488 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1560571 1523.995 1.488 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1561567 1524.968 1.489 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1561951 1525.343 1.490 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1562527 1525.905 1.490 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1564561 1527.892 1.492 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1565457 1528.767 1.493 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1569909 1533.114 1.497 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1571253 1534.427 1.498 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1580871 1543.819 1.508 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1582855 1545.757 1.510 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1603501 1565.919 1.529 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1606509 1568.856 1.532 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1652475 1613.745 1.576 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1656955 1618.120 1.580 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1758175 1716.968 1.677 openf___224_> Open ${LIB}/dist-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1758571 1717.354 1.677 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1759367 1718.132 1.678 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1760163 1718.909 1.679 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1761351 1720.069 1.680 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1761751 1720.460 1.680 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1762351 1721.046 1.681 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1763251 1721.925 1.682 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1764599 1723.241 1.683 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1764799 1723.437 1.683 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1766823 1725.413 1.685 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1767123 1725.706 1.685 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1770159 1728.671 1.688 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1770607 1729.108 1.689 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1775159 1733.554 1.693 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1775831 1734.210 1.694 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1782659 1740.878 1.700 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1783667 1741.862 1.701 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1793911 1751.866 1.711 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1794511 1752.452 1.711 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1794911 1752.843 1.712 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1796423 1754.319 1.713 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1811787 1769.323 1.728 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1812687 1770.202 1.729 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1813287 1770.788 1.729 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1815555 1773.003 1.731 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1838603 1795.511 1.753 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1839947 1796.823 1.755 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1840847 1797.702 1.756 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1844251 1801.026 1.759 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1878823 1834.788 1.792 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1880839 1836.757 1.794 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1882187 1838.073 1.795 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1887291 1843.058 1.800 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1939147 1893.698 1.849 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1942171 1896.651 1.852 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1944195 1898.628 1.854 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 1951851 1906.104 1.861 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2029635 1982.065 1.936 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2034171 1986.495 1.940 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2037207 1989.460 1.943 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2048691 2000.675 1.954 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2165367 2114.616 2.065 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2172171 2121.261 2.072 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2176723 2125.706 2.076 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2193951 2142.530 2.092 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2368967 2313.444 2.259 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2379179 2323.417 2.269 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2386007 2330.085 2.275 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2411847 2355.319 2.300 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2674371 2611.690 2.550 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2689683 2626.644 2.565 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2699927 2636.647 2.575 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 2738687 2674.499 2.612 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3132471 3059.054 2.987 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3155439 3081.483 3.009 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3170803 3096.487 3.024 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3228943 3153.265 3.079 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3819619 3730.097 3.643 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3854071 3763.741 3.676 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3877119 3786.249 3.698 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 3964331 3871.417 3.781 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4850347 4736.667 4.626 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4902031 4787.140 4.675 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4936603 4820.901 4.708 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5067419 4948.651 4.833 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6396443 6246.526 6.100 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 0 0 0 0 12561 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6725023 6567.405 6.413 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6796639 6637.343 6.482 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 12724 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -828.9336 << end of ENERGY. DOPE score : -828.933594 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6503887 6351.452 6.203 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 373 77 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1465 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 53.9595 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 80 0 0 0.008 0.008 1.5519 1.000 2 Bond angle potential : 112 0 0 2.666 2.666 15.266 1.000 3 Stereochemical cosine torsion poten: 70 0 5 43.456 43.456 23.117 1.000 4 Stereochemical improper torsion pot: 36 0 0 1.378 1.378 1.5171 1.000 5 Soft-sphere overlap restraints : 1465 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 11 0 0 5.054 5.054 3.3162 1.000 14 Sidechain Chi_1 dihedral restraints: 9 0 0 69.508 69.508 3.2155 1.000 15 Sidechain Chi_2 dihedral restraints: 7 0 0 73.736 73.736 1.3548 1.000 16 Sidechain Chi_3 dihedral restraints: 2 0 0 39.244 39.244 1.1381 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 12 5 5 36.712 121.687 22.240 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 1465 0 3 1.851 1.851 -18.757 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 305 23I 24Q C N 162 164 -108.33 -121.10 20.40 1.06 -63.80 170.03 27.38 1 24Q 24Q N CA 164 165 155.61 139.70 -40.30 2 306 24Q 25G C N 171 173 -110.41 -80.20 48.34 3.28 82.20 -149.36 16.42 2 25G 25G N CA 173 174 136.36 174.10 8.50 3 307 25G 26S C N 175 177 -174.45 -136.60 65.22 2.32 -64.10 163.52 19.77 3 26S 26S N CA 177 178 -155.68 151.20 -35.00 4 309 27I 28Y C N 189 191 -53.86 -98.40 47.17 2.52 -63.50 156.55 25.34 4 28Y 28Y N CA 191 192 112.85 128.40 -43.40 5 310 28Y 29A C N 201 203 -174.64 -134.00 40.82 1.21 -62.50 -157.78 39.09 5 29A 29A N CA 203 204 150.83 147.00 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 3 5 21 28 33 30 53 44 41 70 << end of ENERGY. openf___224_> Open 1fdx.BL00210001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 13033 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -878.8393 << end of ENERGY. DOPE score : -878.839294 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6503887 6351.452 6.203 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 373 77 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1432 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 49.3945 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 80 0 0 0.007 0.007 1.0946 1.000 2 Bond angle potential : 112 0 0 2.209 2.209 9.9262 1.000 3 Stereochemical cosine torsion poten: 70 0 3 48.548 48.548 25.927 1.000 4 Stereochemical improper torsion pot: 36 0 0 1.469 1.469 1.5993 1.000 5 Soft-sphere overlap restraints : 1432 0 0 0.000 0.000 0.87133E-02 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 11 0 0 4.185 4.185 2.2739 1.000 14 Sidechain Chi_1 dihedral restraints: 9 0 0 94.078 94.078 3.5497 1.000 15 Sidechain Chi_2 dihedral restraints: 7 0 0 81.947 81.947 1.3731 1.000 16 Sidechain Chi_3 dihedral restraints: 2 0 0 80.505 80.505 0.98334 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 12 7 2 36.874 141.379 15.623 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 1432 0 3 1.745 1.745 -12.964 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 300 18C 19P C N 124 126 -69.22 -58.70 19.23 1.15 -64.50 161.67 12.32 1 19P 19P N CA 126 127 -14.40 -30.50 147.20 2 302 20V 21N C N 138 140 -98.77 -119.90 22.52 0.74 -63.20 173.97 19.99 2 21N 21N N CA 140 141 129.20 137.00 -41.10 3 305 23I 24Q C N 162 164 -145.60 -121.10 42.60 1.51 -63.80 166.61 28.71 3 24Q 24Q N CA 164 165 174.55 139.70 -40.30 4 306 24Q 25G C N 171 173 -95.71 -80.20 31.86 0.75 82.20 -116.28 18.80 4 25G 25G N CA 173 174 -158.07 174.10 8.50 5 307 25G 26S C N 175 177 -83.91 -72.40 79.40 5.07 -64.10 110.63 7.08 5 26S 26S N CA 177 178 73.84 152.40 -35.00 6 309 27I 28Y C N 189 191 -87.35 -98.40 16.54 1.33 -63.50 177.51 29.40 6 28Y 28Y N CA 191 192 140.70 128.40 -43.40 7 310 28Y 29A C N 201 203 161.04 -134.00 65.08 2.01 -62.50 -143.35 42.63 7 29A 29A N CA 203 204 150.83 147.00 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 2 5 19 25 33 32 53 41 38 65 << end of ENERGY. openf___224_> Open 1fdx.BL00220001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 12577 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -895.7858 << end of ENERGY. DOPE score : -895.785767 openf___224_> Open 1fdx.IL00000001.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6503887 6351.452 6.203 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 373 77 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. preppdf_457W> Both soft sphere and statistical potential terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1488 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 7.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 64.3671 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 80 0 0 0.010 0.010 2.1018 1.000 2 Bond angle potential : 112 0 0 2.802 2.802 16.623 1.000 3 Stereochemical cosine torsion poten: 70 0 2 45.876 45.876 23.407 1.000 4 Stereochemical improper torsion pot: 36 0 0 2.112 2.112 3.1641 1.000 5 Soft-sphere overlap restraints : 1488 0 0 0.002 0.002 0.42781 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 11 0 0 4.957 4.957 3.1897 1.000 14 Sidechain Chi_1 dihedral restraints: 9 0 2 82.035 82.035 8.3812 1.000 15 Sidechain Chi_2 dihedral restraints: 7 0 0 96.287 96.287 3.3934 1.000 16 Sidechain Chi_3 dihedral restraints: 2 0 0 37.092 37.092 1.2367 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 12 6 3 27.373 130.673 12.414 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 1488 0 3 1.884 1.884 -9.9722 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 302 20V 21N C N 138 140 -95.38 -71.20 27.52 1.63 -63.20 166.10 22.59 1 21N 21N N CA 140 141 155.95 142.80 -41.10 2 303 21N 22I C N 146 148 -74.40 -63.40 11.00 1.96 -120.60 179.87 8.56 2 22I 22I N CA 148 149 -43.53 -43.60 130.30 3 305 23I 24Q C N 162 164 -129.99 -121.10 18.07 0.94 -63.80 177.09 23.20 3 24Q 24Q N CA 164 165 123.96 139.70 -40.30 4 306 24Q 25G C N 171 173 -144.02 -167.20 43.61 1.23 82.20 -174.05 14.31 4 25G 25G N CA 173 174 137.66 174.60 8.50 5 309 27I 28Y C N 189 191 -60.78 -98.40 40.73 2.33 -63.50 156.23 24.94 5 28Y 28Y N CA 191 192 112.81 128.40 -43.40 6 310 28Y 29A C N 201 203 -173.54 -134.00 39.72 1.18 -62.50 -158.39 38.94 6 29A 29A N CA 203 204 150.83 147.00 -40.90 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 1 5 20 29 33 32 54 42 44 66 << end of ENERGY. openf___224_> Open 1fdx.BL00230001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: ASP:OXT ASP >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 77 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 339 339 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 13521 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -941.5539 << end of ENERGY. DOPE score : -941.553894 >> Summary of successfully produced loop models: Filename molpdf DOPE score ------------------------------------------------------- 1fdx.BL00200001.pdb 73.02764 -828.93359 1fdx.BL00210001.pdb 53.95946 -878.83929 1fdx.BL00220001.pdb 49.39454 -895.78577 1fdx.BL00230001.pdb 64.36712 -941.55389 Dynamically allocated memory at finish [B,KiB,MiB]: 6441911 6290.929 6.143 Starting time : 2016/04/05 22:38:51 Closing time : 2016/04/05 22:39:07 Total CPU time [seconds] : 16.44