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 22:42:12 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 amaxrestraints [B,KiB,MiB]: 652987 637.683 0.623 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 762391 744.522 0.727 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1064115 1039.175 1.015 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 55 Number of all, selected real atoms : 380 380 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 1 1 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 623 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 : 0.1219 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 : 1 0 0 0.023 0.023 0.12195 1.000 2 Bond angle potential : 0 0 0 0.000 0.000 0.0000 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.0000 1.000 5 Soft-sphere overlap restraints : 623 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: 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. 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 0 1 1 9 13 20 24 61 40 56 << end of ENERGY. preppdf_449W> No atoms selected; no restraints will be selected. spline__463_> Number of splined restraints: 1 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 55 Number of all, selected real atoms : 380 380 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 2 1 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 623 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 : 0.1249 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 : 1 0 0 0.025 0.025 0.12489 1.000 2 Bond angle potential : 0 0 0 0.000 0.000 0.0000 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.0000 1.000 5 Soft-sphere overlap restraints : 623 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: 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. 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 0 1 1 9 13 20 24 61 40 56 << end of ENERGY. Dynamically allocated memory at finish [B,KiB,MiB]: 1064115 1039.175 1.015 Starting time : 2016/04/05 22:42:12 Closing time : 2016/04/05 22:42:12 Total CPU time [seconds] : 0.29