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 22:41:59 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 pick_re_612_> Number of MODEL atoms, selected restraints; 468 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 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): 471 Dynamic pairs routine : 1, NATM x NATM double loop Optimization method (OPTIMIZATON_METHOD) : 1 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Atomic shift for convergence (MIN_ATOM_SHIFT) : 0.010 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 2 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 All restraint types and their scaling factors : 1 Bond length potential : 0.0100 2 Bond angle potential : 0.0100 3 Stereochemical cosine torsion potential : 0.0100 4 Stereochemical improper torsion potentia : 0.0100 5 Soft-sphere overlap restraints : 0.0100 6 Lennard-Jones 6-12 potential : 0.0100 7 Coulomb point-point electrostatic potent : 0.0100 8 H-bonding potential : 0.0100 9 Distance restraints 1 (CA-CA) : 0.0100 10 Distance restraints 2 (N-O) : 0.0100 11 Mainchain Phi dihedral restraints : 0.0100 12 Mainchain Psi dihedral restraints : 0.0100 13 Mainchain Omega dihedral restraints : 0.0100 14 Sidechain Chi_1 dihedral restraints : 0.0100 15 Sidechain Chi_2 dihedral restraints : 0.0100 16 Sidechain Chi_3 dihedral restraints : 0.0100 17 Sidechain Chi_4 dihedral restraints : 0.0100 18 Disulfide distance restraints : 0.0100 19 Disulfide angle restraints : 0.0100 20 Disulfide dihedral angle restraints : 0.0100 21 Lower bound distance restraints : 0.0100 22 Upper bound distance restraints : 0.0100 23 Distance restraints 3 (SDCH-MNCH) : 0.0100 24 Sidechain Chi_5 dihedral restraints : 0.0100 25 Phi/Psi pair of dihedral restraints : 0.0100 26 Distance restraints 4 (SDCH-SDCH) : 0.0100 27 Distance restraints 5 (X-Y) : 0.0100 28 NMR distance restraints 6 (X-Y) : 0.0100 29 NMR distance restraints 7 (X-Y) : 0.0100 30 Minimal distance restraints : 0.0100 31 Non-bonded restraints : 0.0100 32 Atomic accessibility restraints : 0.0100 33 Atomic density restraints : 0.0100 34 Absolute position restraints : 0.0100 35 Dihedral angle difference restraints : 0.0100 36 GBSA implicit solvent potential : 0.0100 37 EM density fitting potential : 0.0100 38 SAXS restraints : 0.0100 39 Symmetry restraints : 0.0100 Initial value of energy before optimization : 4.8476 Current energy : 1.9579 Optimizer exit status : 0 Number of iterations : 58 Number of calls to energy function : 119 Number of updates of dynamic contacts : 5 Number of non-updates of dynamic contacts : 115 Final maximal atomic shift : 0.009 pick_re_612_> Number of MODEL atoms, selected restraints; 468 2061 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): 533 Dynamic pairs routine : 1, NATM x NATM double loop Optimization method (OPTIMIZATON_METHOD) : 1 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Atomic shift for convergence (MIN_ATOM_SHIFT) : 0.010 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 5 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 All restraint types and their scaling factors : 1 Bond length potential : 0.1000 2 Bond angle potential : 0.1000 3 Stereochemical cosine torsion potential : 0.1000 4 Stereochemical improper torsion potentia : 0.1000 5 Soft-sphere overlap restraints : 0.1000 6 Lennard-Jones 6-12 potential : 0.1000 7 Coulomb point-point electrostatic potent : 0.1000 8 H-bonding potential : 0.1000 9 Distance restraints 1 (CA-CA) : 0.1000 10 Distance restraints 2 (N-O) : 0.1000 11 Mainchain Phi dihedral restraints : 0.1000 12 Mainchain Psi dihedral restraints : 0.1000 13 Mainchain Omega dihedral restraints : 0.1000 14 Sidechain Chi_1 dihedral restraints : 0.1000 15 Sidechain Chi_2 dihedral restraints : 0.1000 16 Sidechain Chi_3 dihedral restraints : 0.1000 17 Sidechain Chi_4 dihedral restraints : 0.1000 18 Disulfide distance restraints : 0.1000 19 Disulfide angle restraints : 0.1000 20 Disulfide dihedral angle restraints : 0.1000 21 Lower bound distance restraints : 0.1000 22 Upper bound distance restraints : 0.1000 23 Distance restraints 3 (SDCH-MNCH) : 0.1000 24 Sidechain Chi_5 dihedral restraints : 0.1000 25 Phi/Psi pair of dihedral restraints : 0.1000 26 Distance restraints 4 (SDCH-SDCH) : 0.1000 27 Distance restraints 5 (X-Y) : 0.1000 28 NMR distance restraints 6 (X-Y) : 0.1000 29 NMR distance restraints 7 (X-Y) : 0.1000 30 Minimal distance restraints : 0.1000 31 Non-bonded restraints : 0.1000 32 Atomic accessibility restraints : 0.1000 33 Atomic density restraints : 0.1000 34 Absolute position restraints : 0.1000 35 Dihedral angle difference restraints : 0.1000 36 GBSA implicit solvent potential : 0.1000 37 EM density fitting potential : 0.1000 38 SAXS restraints : 0.1000 39 Symmetry restraints : 0.1000 Initial value of energy before optimization : 19.9325 Current energy : 19.4457 Optimizer exit status : 0 Number of iterations : 7 Number of calls to energy function : 15 Number of updates of dynamic contacts : 1 Number of non-updates of dynamic contacts : 15 Final maximal atomic shift : 0.008 pick_re_612_> Number of MODEL atoms, selected restraints; 468 2061 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): 575 Dynamic pairs routine : 1, NATM x NATM double loop Optimization method (OPTIMIZATON_METHOD) : 1 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Atomic shift for convergence (MIN_ATOM_SHIFT) : 0.010 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 10 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 All restraint types and their scaling factors : 1 Bond length potential : 0.2000 2 Bond angle potential : 0.2000 3 Stereochemical cosine torsion potential : 0.2000 4 Stereochemical improper torsion potentia : 0.2000 5 Soft-sphere overlap restraints : 0.2000 6 Lennard-Jones 6-12 potential : 0.2000 7 Coulomb point-point electrostatic potent : 0.2000 8 H-bonding potential : 0.2000 9 Distance restraints 1 (CA-CA) : 0.2000 10 Distance restraints 2 (N-O) : 0.2000 11 Mainchain Phi dihedral restraints : 0.2000 12 Mainchain Psi dihedral restraints : 0.2000 13 Mainchain Omega dihedral restraints : 0.2000 14 Sidechain Chi_1 dihedral restraints : 0.2000 15 Sidechain Chi_2 dihedral restraints : 0.2000 16 Sidechain Chi_3 dihedral restraints : 0.2000 17 Sidechain Chi_4 dihedral restraints : 0.2000 18 Disulfide distance restraints : 0.2000 19 Disulfide angle restraints : 0.2000 20 Disulfide dihedral angle restraints : 0.2000 21 Lower bound distance restraints : 0.2000 22 Upper bound distance restraints : 0.2000 23 Distance restraints 3 (SDCH-MNCH) : 0.2000 24 Sidechain Chi_5 dihedral restraints : 0.2000 25 Phi/Psi pair of dihedral restraints : 0.2000 26 Distance restraints 4 (SDCH-SDCH) : 0.2000 27 Distance restraints 5 (X-Y) : 0.2000 28 NMR distance restraints 6 (X-Y) : 0.2000 29 NMR distance restraints 7 (X-Y) : 0.2000 30 Minimal distance restraints : 0.2000 31 Non-bonded restraints : 0.2000 32 Atomic accessibility restraints : 0.2000 33 Atomic density restraints : 0.2000 34 Absolute position restraints : 0.2000 35 Dihedral angle difference restraints : 0.2000 36 GBSA implicit solvent potential : 0.2000 37 EM density fitting potential : 0.2000 38 SAXS restraints : 0.2000 39 Symmetry restraints : 0.2000 Initial value of energy before optimization : 131.1202 Current energy : 34.5346 Optimizer exit status : 0 Number of iterations : 68 Number of calls to energy function : 138 Number of updates of dynamic contacts : 7 Number of non-updates of dynamic contacts : 132 Final maximal atomic shift : 0.009 pick_re_612_> Number of MODEL atoms, selected restraints; 468 2061 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): 844 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 1 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Atomic shift for convergence (MIN_ATOM_SHIFT) : 0.010 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 50 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 All restraint types and their scaling factors : 1 Bond length potential : 0.5000 2 Bond angle potential : 0.5000 3 Stereochemical cosine torsion potential : 0.5000 4 Stereochemical improper torsion potentia : 0.5000 5 Soft-sphere overlap restraints : 0.5000 6 Lennard-Jones 6-12 potential : 0.5000 7 Coulomb point-point electrostatic potent : 0.5000 8 H-bonding potential : 0.5000 9 Distance restraints 1 (CA-CA) : 0.5000 10 Distance restraints 2 (N-O) : 0.5000 11 Mainchain Phi dihedral restraints : 0.5000 12 Mainchain Psi dihedral restraints : 0.5000 13 Mainchain Omega dihedral restraints : 0.5000 14 Sidechain Chi_1 dihedral restraints : 0.5000 15 Sidechain Chi_2 dihedral restraints : 0.5000 16 Sidechain Chi_3 dihedral restraints : 0.5000 17 Sidechain Chi_4 dihedral restraints : 0.5000 18 Disulfide distance restraints : 0.5000 19 Disulfide angle restraints : 0.5000 20 Disulfide dihedral angle restraints : 0.5000 21 Lower bound distance restraints : 0.5000 22 Upper bound distance restraints : 0.5000 23 Distance restraints 3 (SDCH-MNCH) : 0.5000 24 Sidechain Chi_5 dihedral restraints : 0.5000 25 Phi/Psi pair of dihedral restraints : 0.5000 26 Distance restraints 4 (SDCH-SDCH) : 0.5000 27 Distance restraints 5 (X-Y) : 0.5000 28 NMR distance restraints 6 (X-Y) : 0.5000 29 NMR distance restraints 7 (X-Y) : 0.5000 30 Minimal distance restraints : 0.5000 31 Non-bonded restraints : 0.5000 32 Atomic accessibility restraints : 0.5000 33 Atomic density restraints : 0.5000 34 Absolute position restraints : 0.5000 35 Dihedral angle difference restraints : 0.5000 36 GBSA implicit solvent potential : 0.5000 37 EM density fitting potential : 0.5000 38 SAXS restraints : 0.5000 39 Symmetry restraints : 0.5000 Initial value of energy before optimization : 1106.0768 Current energy : 89.1649 Optimizer exit status : 0 Number of iterations : 38 Number of calls to energy function : 78 Number of updates of dynamic contacts : 6 Number of non-updates of dynamic contacts : 73 Final maximal atomic shift : 0.003 pick_re_612_> Number of MODEL atoms, selected restraints; 468 2061 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): 895 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 1 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Atomic shift for convergence (MIN_ATOM_SHIFT) : 0.010 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 9999 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 All restraint types and their scaling factors : 1 Bond length potential : 1.0000 2 Bond angle potential : 1.0000 3 Stereochemical cosine torsion potential : 1.0000 4 Stereochemical improper torsion potentia : 1.0000 5 Soft-sphere overlap restraints : 1.0000 6 Lennard-Jones 6-12 potential : 1.0000 7 Coulomb point-point electrostatic potent : 1.0000 8 H-bonding potential : 1.0000 9 Distance restraints 1 (CA-CA) : 1.0000 10 Distance restraints 2 (N-O) : 1.0000 11 Mainchain Phi dihedral restraints : 1.0000 12 Mainchain Psi dihedral restraints : 1.0000 13 Mainchain Omega dihedral restraints : 1.0000 14 Sidechain Chi_1 dihedral restraints : 1.0000 15 Sidechain Chi_2 dihedral restraints : 1.0000 16 Sidechain Chi_3 dihedral restraints : 1.0000 17 Sidechain Chi_4 dihedral restraints : 1.0000 18 Disulfide distance restraints : 1.0000 19 Disulfide angle restraints : 1.0000 20 Disulfide dihedral angle restraints : 1.0000 21 Lower bound distance restraints : 1.0000 22 Upper bound distance restraints : 1.0000 23 Distance restraints 3 (SDCH-MNCH) : 1.0000 24 Sidechain Chi_5 dihedral restraints : 1.0000 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 36 GBSA implicit solvent potential : 1.0000 37 EM density fitting potential : 1.0000 38 SAXS restraints : 1.0000 39 Symmetry restraints : 1.0000 Initial value of energy before optimization : 192.6080 Current energy : 177.7198 Optimizer exit status : 0 Number of iterations : 15 Number of calls to energy function : 31 Number of updates of dynamic contacts : 1 Number of non-updates of dynamic contacts : 31 Final maximal atomic shift : 0.009 pick_re_612_> Number of MODEL atoms, selected restraints; 468 2061 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): 708 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 3 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 9999 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 All restraint types and their scaling factors : 1 Bond length potential : 1.0000 2 Bond angle potential : 1.0000 3 Stereochemical cosine torsion potential : 1.0000 4 Stereochemical improper torsion potentia : 1.0000 5 Soft-sphere overlap restraints : 1.0000 6 Lennard-Jones 6-12 potential : 1.0000 7 Coulomb point-point electrostatic potent : 1.0000 8 H-bonding potential : 1.0000 9 Distance restraints 1 (CA-CA) : 1.0000 10 Distance restraints 2 (N-O) : 1.0000 11 Mainchain Phi dihedral restraints : 1.0000 12 Mainchain Psi dihedral restraints : 1.0000 13 Mainchain Omega dihedral restraints : 1.0000 14 Sidechain Chi_1 dihedral restraints : 1.0000 15 Sidechain Chi_2 dihedral restraints : 1.0000 16 Sidechain Chi_3 dihedral restraints : 1.0000 17 Sidechain Chi_4 dihedral restraints : 1.0000 18 Disulfide distance restraints : 1.0000 19 Disulfide angle restraints : 1.0000 20 Disulfide dihedral angle restraints : 1.0000 21 Lower bound distance restraints : 1.0000 22 Upper bound distance restraints : 1.0000 23 Distance restraints 3 (SDCH-MNCH) : 1.0000 24 Sidechain Chi_5 dihedral restraints : 1.0000 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 36 GBSA implicit solvent potential : 1.0000 37 EM density fitting potential : 1.0000 38 SAXS restraints : 1.0000 39 Symmetry restraints : 1.0000 Initial value of energy before optimization : 177.7198 Current energy : 399.9676 Number of iterations : 200 Number of calls to energy function : 201 Number of updates of dynamic contacts : 31 Number of non-updates of dynamic contacts : 170 Final maximal atomic shift : 0.064 TEMPERATURE : 300.000 EQUILIBRATE : 999999 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.200 Maximal energy, step : 429.0599 21 Minimal energy, step : 177.7198 0 Average energy, stand.dev. : 392.7938 0.0000 Average atomic shift along one axis : 0.023 MODEL returned : FINAL pick_re_612_> Number of MODEL atoms, selected restraints; 468 2061 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): 634 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 3 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 9999 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 All restraint types and their scaling factors : 1 Bond length potential : 1.0000 2 Bond angle potential : 1.0000 3 Stereochemical cosine torsion potential : 1.0000 4 Stereochemical improper torsion potentia : 1.0000 5 Soft-sphere overlap restraints : 1.0000 6 Lennard-Jones 6-12 potential : 1.0000 7 Coulomb point-point electrostatic potent : 1.0000 8 H-bonding potential : 1.0000 9 Distance restraints 1 (CA-CA) : 1.0000 10 Distance restraints 2 (N-O) : 1.0000 11 Mainchain Phi dihedral restraints : 1.0000 12 Mainchain Psi dihedral restraints : 1.0000 13 Mainchain Omega dihedral restraints : 1.0000 14 Sidechain Chi_1 dihedral restraints : 1.0000 15 Sidechain Chi_2 dihedral restraints : 1.0000 16 Sidechain Chi_3 dihedral restraints : 1.0000 17 Sidechain Chi_4 dihedral restraints : 1.0000 18 Disulfide distance restraints : 1.0000 19 Disulfide angle restraints : 1.0000 20 Disulfide dihedral angle restraints : 1.0000 21 Lower bound distance restraints : 1.0000 22 Upper bound distance restraints : 1.0000 23 Distance restraints 3 (SDCH-MNCH) : 1.0000 24 Sidechain Chi_5 dihedral restraints : 1.0000 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 36 GBSA implicit solvent potential : 1.0000 37 EM density fitting potential : 1.0000 38 SAXS restraints : 1.0000 39 Symmetry restraints : 1.0000 Initial value of energy before optimization : 399.9676 Current energy : 417.0089 Number of iterations : 200 Number of calls to energy function : 201 Number of updates of dynamic contacts : 31 Number of non-updates of dynamic contacts : 170 Final maximal atomic shift : 0.066 TEMPERATURE : 200.000 EQUILIBRATE : 999999 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.200 Maximal energy, step : 466.6061 48 Minimal energy, step : 388.1084 1 Average energy, stand.dev. : 436.0814 0.0000 Average atomic shift along one axis : 0.024 MODEL returned : FINAL pick_re_612_> Number of MODEL atoms, selected restraints; 468 2061 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): 641 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 3 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Maximal number of iterations (MAX_ITERATIONS) : 200 RESIDUE_SPAN_RANGE : 0 9999 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 All restraint types and their scaling factors : 1 Bond length potential : 1.0000 2 Bond angle potential : 1.0000 3 Stereochemical cosine torsion potential : 1.0000 4 Stereochemical improper torsion potentia : 1.0000 5 Soft-sphere overlap restraints : 1.0000 6 Lennard-Jones 6-12 potential : 1.0000 7 Coulomb point-point electrostatic potent : 1.0000 8 H-bonding potential : 1.0000 9 Distance restraints 1 (CA-CA) : 1.0000 10 Distance restraints 2 (N-O) : 1.0000 11 Mainchain Phi dihedral restraints : 1.0000 12 Mainchain Psi dihedral restraints : 1.0000 13 Mainchain Omega dihedral restraints : 1.0000 14 Sidechain Chi_1 dihedral restraints : 1.0000 15 Sidechain Chi_2 dihedral restraints : 1.0000 16 Sidechain Chi_3 dihedral restraints : 1.0000 17 Sidechain Chi_4 dihedral restraints : 1.0000 18 Disulfide distance restraints : 1.0000 19 Disulfide angle restraints : 1.0000 20 Disulfide dihedral angle restraints : 1.0000 21 Lower bound distance restraints : 1.0000 22 Upper bound distance restraints : 1.0000 23 Distance restraints 3 (SDCH-MNCH) : 1.0000 24 Sidechain Chi_5 dihedral restraints : 1.0000 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 36 GBSA implicit solvent potential : 1.0000 37 EM density fitting potential : 1.0000 38 SAXS restraints : 1.0000 39 Symmetry restraints : 1.0000 Initial value of energy before optimization : 417.0089 Current energy : 391.9370 Number of iterations : 200 Number of calls to energy function : 201 Number of updates of dynamic contacts : 30 Number of non-updates of dynamic contacts : 171 Final maximal atomic shift : 0.054 TEMPERATURE : 100.000 EQUILIBRATE : 999999 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.200 Maximal energy, step : 424.8559 2 Minimal energy, step : 364.8123 177 Average energy, stand.dev. : 389.6258 0.0000 Average atomic shift along one axis : 0.022 MODEL returned : FINAL openf___224_> Open 1fas.B wrpdb___568_> Residues, atoms, selected atoms: 61 468 468 Dynamically allocated memory at finish [B,KiB,MiB]: 1190243 1162.347 1.135 Starting time : 2016/04/05 22:41:59 Closing time : 2016/04/05 22:42:00 Total CPU time [seconds] : 1.03