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 22:42:14 read_to_681_> topology.submodel read from topology file: 3 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): 826 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) : 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 : 1143.9458 Current energy : 816.0462 Number of iterations : 100 Number of calls to energy function : 101 Number of updates of dynamic contacts : 34 Number of non-updates of dynamic contacts : 67 Final maximal atomic shift : 0.136 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 : 1143.9458 0 Minimal energy, step : 726.8572 2 Average energy, stand.dev. : 796.8010 0.0000 Average atomic shift along one axis : 0.037 MODEL returned : FINAL Total CPU time [seconds] : 0.50