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 22:42:03 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]: 393422 384.201 0.375 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 395022 385.764 0.377 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 399002 389.650 0.381 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 401002 391.604 0.382 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 404002 394.533 0.385 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 408502 398.928 0.390 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 414074 404.369 0.395 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 416874 407.104 0.398 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 421074 411.205 0.402 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 427374 417.357 0.408 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 430146 420.064 0.410 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 431546 421.432 0.412 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open ../atom_files/pdb1fas.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 442499 432.128 0.422 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 442575 432.202 0.422 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 442746 432.369 0.422 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 443596 433.199 0.423 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 444854 434.428 0.424 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 446758 436.287 0.426 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 446798 436.326 0.426 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 446888 436.414 0.426 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 449744 439.203 0.429 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 449804 439.262 0.429 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 449939 439.394 0.429 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 454223 443.577 0.433 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 454311 443.663 0.433 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 454509 443.856 0.433 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 460935 450.132 0.440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 506663 494.788 0.483 read_mo_297_> Segments, residues, atoms: 1 61 468 read_mo_298_> Segment: 1 1 A 61 A 468 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 508964 497.035 0.485 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 543981 531.231 0.519 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 544694 531.928 0.519 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 579711 566.124 0.553 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 586615 572.866 0.559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 61 467 477 0 0 193 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 606591 592.374 0.578 patch_______> segment topology patched using RTF: 1 ; THR ; NTER segments residues atoms bonds angles dihedrals impropers: 1 61 467 477 643 768 193 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 628127 613.405 0.599 patch_______> segment topology patched using RTF: 61 ; TYR ; CTER segments residues atoms bonds angles dihedrals impropers: 1 61 468 478 645 770 194 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 61 468 478 645 770 194 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: 468 0 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 662108 646.590 0.631 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 670300 654.590 0.639 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 686684 670.590 0.655 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 719452 702.590 0.686 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 752220 734.590 0.717 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 478 645 749 189 Total number of restraints before, now : 0 2061 make_re_422_> Number of previous, current restraints : 0 2061 make_re_423_> Number of previous, current selected restraints: 0 2061 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 886407 865.632 0.845 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1190243 1162.347 1.135 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 61 Number of all, selected real atoms : 468 468 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 2061 2061 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 804 Dynamic pairs routine : 2, NATM x NATM cell sorting 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 : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1143.9458 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 : 478 0 1 0.025 0.025 93.042 1.000 2 Bond angle potential : 645 0 0 3.501 3.501 153.55 1.000 3 Stereochemical cosine torsion poten: 749 4 19 53.726 53.726 229.26 1.000 4 Stereochemical improper torsion pot: 189 0 0 1.217 1.217 8.9101 1.000 5 Soft-sphere overlap restraints : 804 4 4 0.083 0.083 659.18 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: 0 0 0 0.000 0.000 0.0000 1.000 14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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: 0 0 0 0.000 0.000 0.0000 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 : 0 0 0 0.000 0.000 0.0000 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 3 : Stereochemical cosine torsion potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1511 31P 31P CA CB 241 243 -40.49 34.59 -75.08 7.43 34.59 -75.08 7.43 2 1632 42P 42P CA CB 315 317 -42.34 34.59 -76.93 7.74 34.59 -76.93 7.74 3 1651 43P 43P CA CB 322 324 -45.13 34.59 -79.72 8.22 34.59 -79.72 8.22 4 1807 56P 56P CA CB 419 421 -36.26 34.59 -70.85 6.72 34.59 -70.85 6.72 report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 19 160 2.032 serious non-bonded atom clash: 127 301 2.020 serious non-bonded atom clash: 311 396 2.009 serious non-bonded atom clash: 402 445 2.024 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: 4 0 0 0 0 0 1 5 17 23 29 31 45 49 64 << end of ENERGY. pick_re_612_> Number of MODEL atoms, selected restraints; 244 2061 rmdupl__427_> 94 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 2061 1967 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 61 Number of all, selected real atoms : 468 244 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 1967 1967 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 673 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 : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 478.3114 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 : 478 0 1 0.025 0.025 93.042 1.000 2 Bond angle potential : 645 0 0 3.501 3.501 153.55 1.000 3 Stereochemical cosine torsion poten: 655 4 19 55.981 55.981 222.30 1.000 4 Stereochemical improper torsion pot: 189 0 0 1.217 1.217 8.9101 1.000 5 Soft-sphere overlap restraints : 673 0 0 0.003 0.003 0.50586 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: 0 0 0 0.000 0.000 0.0000 1.000 14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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: 0 0 0 0.000 0.000 0.0000 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 : 0 0 0 0.000 0.000 0.0000 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 3 : Stereochemical cosine torsion potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1465 31P 31P CA CB 241 243 -40.49 34.59 -75.08 7.43 34.59 -75.08 7.43 2 1565 42P 42P CA CB 315 317 -42.34 34.59 -76.93 7.74 34.59 -76.93 7.74 3 1580 43P 43P CA CB 322 324 -45.13 34.59 -79.72 8.22 34.59 -79.72 8.22 4 1717 56P 56P CA CB 419 421 -36.26 34.59 -70.85 6.72 34.59 -70.85 6.72 report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 19 160 2.032 serious non-bonded atom clash: 127 301 2.020 serious non-bonded atom clash: 311 396 2.009 serious non-bonded atom clash: 402 445 2.024 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: 4 0 0 0 0 0 1 5 17 23 29 31 45 49 64 << end of ENERGY. openf___224_> Open 1fas.rsr Dynamically allocated memory at finish [B,KiB,MiB]: 1190243 1162.347 1.135 Starting time : 2016/04/05 22:42:03 Closing time : 2016/04/05 22:42:03 Total CPU time [seconds] : 0.35