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 22:42:15 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/pdb1fdn.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 55 380 read_mo_298_> Segment: 1 1 A 55 A 380 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 508790 496.865 0.485 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 538937 526.306 0.514 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 539596 526.949 0.515 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 569743 556.390 0.543 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 575263 561.780 0.549 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 55 379 384 0 0 153 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 591623 577.757 0.564 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 55 379 384 527 629 153 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 609599 595.312 0.581 patch_______> segment topology patched using RTF: 55 ; ALA ; CTER segments residues atoms bonds angles dihedrals impropers: 1 55 380 385 529 631 154 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 55 380 385 529 631 154 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: 380 0 Dynamically allocated memory at amaxpseudo_atom [B,KiB,MiB]: 546735 533.921 0.521 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 653203 637.894 0.623 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 661956 646.441 0.631 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 678340 662.441 0.647 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 711108 694.441 0.678 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 385 529 608 150 Total number of restraints before, now : 56 1728 make_re_422_> Number of previous, current restraints : 56 1728 make_re_423_> Number of previous, current selected restraints: 56 1728 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 819951 800.733 0.782 Dynamically allocated memory at amaxpseudo_atom [B,KiB,MiB]: 1112719 1086.640 1.061 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1121831 1095.538 1.070 Number of all residues in MODEL : 55 Number of all, selected real atoms : 380 380 Number of all, selected pseudo atoms : 1 1 Number of all static, selected restraints : 1728 1728 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 983 Dynamic pairs routine : 5, NATM_SEL 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) : 100 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 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 : 2455.8953 Current energy : 501.8671 Optimizer exit status : 1 Number of iterations : 50 Number of calls to energy function : 101 Number of updates of dynamic contacts : 14 Number of non-updates of dynamic contacts : 88 Final maximal atomic shift : 0.065 openf___224_> Open 1fas.ini wrpdb___568_> Residues, atoms, selected atoms: 55 380 380 Dynamically allocated memory at finish [B,KiB,MiB]: 1121831 1095.538 1.070 Starting time : 2016/04/05 22:42:15 Closing time : 2016/04/05 22:42:16 Total CPU time [seconds] : 0.40