Starting phenix.real_space_refine on Mon Sep 14 13:27:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bve_30217/09_2026/7bve_30217.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16931 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 56 5.16 5 C 11038 2.51 5 N 2936 2.21 5 O 3110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17146 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7888 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 958} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7888 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 958} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "D" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CA': 1, '95E': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {' CA': 1, '95E': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 3.54, per 1000 atoms: 0.21 Number of scatterers: 17146 At special positions: 0 Unit cell: (127.1, 117.26, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 56 16.00 P 4 15.00 O 3110 8.00 N 2936 7.00 C 11038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 730 " - pdb=" SG CYS A 973 " distance=2.75 Simple disulfide: pdb=" SG CYS B 730 " - pdb=" SG CYS B 973 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 792.5 milliseconds 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4100 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 19 sheets defined 45.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 13 through 33 removed outlier: 3.790A pdb=" N ALA A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.080A pdb=" N GLY A 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 80 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 213 through 239 Processing helix chain 'A' and resid 257 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.701A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.304A pdb=" N GLY A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.586A pdb=" N ARG A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 349 Processing helix chain 'A' and resid 360 through 379 removed outlier: 4.200A pdb=" N ALA A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 406 removed outlier: 3.507A pdb=" N ALA A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 423 removed outlier: 3.845A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.914A pdb=" N ILE A 429 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 430 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.642A pdb=" N ALA A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Proline residue: A 461 - end of helix Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 478 through 493 removed outlier: 3.675A pdb=" N GLU A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 501 through 509 removed outlier: 4.091A pdb=" N TYR A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 540 Processing helix chain 'A' and resid 547 through 565 removed outlier: 3.777A pdb=" N SER A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 573 through 580 removed outlier: 3.716A pdb=" N GLY A 577 " --> pdb=" O HIS A 574 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 578 " --> pdb=" O HIS A 575 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 580 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 removed outlier: 4.064A pdb=" N CYS A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 620 removed outlier: 3.594A pdb=" N PHE A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 669 removed outlier: 3.584A pdb=" N GLY A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 686 removed outlier: 3.621A pdb=" N VAL A 686 " --> pdb=" O GLN A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 711 removed outlier: 3.828A pdb=" N GLN A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 730 through 734 removed outlier: 4.141A pdb=" N ALA A 733 " --> pdb=" O CYS A 730 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 734 " --> pdb=" O GLY A 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 730 through 734' Processing helix chain 'A' and resid 882 through 888 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 994 through 1002 removed outlier: 3.637A pdb=" N ALA A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1011 through 1014 removed outlier: 3.505A pdb=" N GLY A1014 " --> pdb=" O GLY A1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1011 through 1014' Processing helix chain 'A' and resid 1015 through 1019 Processing helix chain 'B' and resid 12 through 33 removed outlier: 3.884A pdb=" N ARG B 16 " --> pdb=" O HIS B 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 74 through 81 removed outlier: 4.098A pdb=" N GLY B 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 80 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL B 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.938A pdb=" N ASN B 122 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 123 " --> pdb=" O VAL B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 123' Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 213 through 239 Processing helix chain 'B' and resid 257 through 273 Processing helix chain 'B' and resid 280 through 294 removed outlier: 4.702A pdb=" N GLU B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N HIS B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 4.309A pdb=" N GLY B 304 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 326 through 348 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 361 through 379 Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 384 through 406 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.927A pdb=" N ILE B 429 " --> pdb=" O PRO B 426 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 430 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 removed outlier: 3.800A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.626A pdb=" N ALA B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 449 " --> pdb=" O ILE B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 468 Proline residue: B 461 - end of helix Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.752A pdb=" N GLU B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 500 Processing helix chain 'B' and resid 501 through 509 removed outlier: 4.176A pdb=" N TYR B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 540 Processing helix chain 'B' and resid 547 through 565 removed outlier: 3.782A pdb=" N SER B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.730A pdb=" N GLY B 577 " --> pdb=" O HIS B 574 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 578 " --> pdb=" O HIS B 575 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 580 " --> pdb=" O GLY B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 593 removed outlier: 4.009A pdb=" N CYS B 585 " --> pdb=" O GLY B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 620 removed outlier: 3.593A pdb=" N PHE B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 669 removed outlier: 3.584A pdb=" N GLY B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 686 removed outlier: 3.547A pdb=" N ARG B 683 " --> pdb=" O ARG B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 711 removed outlier: 3.505A pdb=" N VAL B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 724 Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 730 through 734 removed outlier: 3.896A pdb=" N ASN B 734 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 888 Processing helix chain 'B' and resid 951 through 955 Processing helix chain 'B' and resid 994 through 1002 Processing helix chain 'B' and resid 1003 through 1005 No H-bonds generated for 'chain 'B' and resid 1003 through 1005' Processing helix chain 'B' and resid 1011 through 1014 removed outlier: 3.504A pdb=" N GLY B1014 " --> pdb=" O GLY B1011 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1014' Processing helix chain 'B' and resid 1015 through 1019 Processing helix chain 'C' and resid 4 through 20 removed outlier: 4.568A pdb=" N ALA C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 11 " --> pdb=" O GLU C 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 69 through 81 Processing helix chain 'D' and resid 4 through 20 removed outlier: 4.568A pdb=" N ALA D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 69 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.590A pdb=" N TYR A 140 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 67 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.304A pdb=" N VAL A 90 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 111 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 92 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 110 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 117 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 118 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL A 126 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL A 120 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 949 through 950B Processing sheet with id=AA6, first strand: chain 'A' and resid 748 through 749 removed outlier: 4.496A pdb=" N THR A 748 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 762 through 764 removed outlier: 3.639A pdb=" N LEU A 764 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 845 " --> pdb=" O LEU A 764 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 833 through 834 Processing sheet with id=AA9, first strand: chain 'A' and resid 862 through 867 Processing sheet with id=AB1, first strand: chain 'A' and resid 961 through 963 removed outlier: 3.539A pdb=" N SER A1039 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU A1040 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 175 removed outlier: 3.609A pdb=" N TYR B 140 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP B 67 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.295A pdb=" N VAL B 90 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG B 111 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 92 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU B 110 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 117 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 949 through 950B Processing sheet with id=AB7, first strand: chain 'B' and resid 748 through 749 removed outlier: 4.482A pdb=" N THR B 748 " --> pdb=" O ARG B 852 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 762 through 764 removed outlier: 3.649A pdb=" N LEU B 764 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 845 " --> pdb=" O LEU B 764 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 862 through 867 Processing sheet with id=AC1, first strand: chain 'B' and resid 961 through 963 removed outlier: 3.531A pdb=" N SER B1039 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B1040 " --> pdb=" O VAL B1025 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2756 1.27 - 1.41: 4406 1.41 - 1.54: 10296 1.54 - 1.68: 46 1.68 - 1.82: 94 Bond restraints: 17598 Sorted by residual: bond pdb=" C2 95E B1103 " pdb=" O1 95E B1103 " ideal model delta sigma weight residual 1.412 1.182 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 95E A1103 " pdb=" O1 95E A1103 " ideal model delta sigma weight residual 1.412 1.182 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C11 95E A1103 " pdb=" O12 95E A1103 " ideal model delta sigma weight residual 1.412 1.185 0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C11 95E B1103 " pdb=" O12 95E B1103 " ideal model delta sigma weight residual 1.412 1.186 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C VAL B 118 " pdb=" O VAL B 118 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.03e-02 9.43e+03 7.91e+01 ... (remaining 17593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 23521 3.24 - 6.48: 494 6.48 - 9.71: 79 9.71 - 12.95: 9 12.95 - 16.19: 1 Bond angle restraints: 24104 Sorted by residual: angle pdb=" N ASP B 931 " pdb=" CA ASP B 931 " pdb=" C ASP B 931 " ideal model delta sigma weight residual 108.31 124.50 -16.19 1.52e+00 4.33e-01 1.13e+02 angle pdb=" CA ASP B 931 " pdb=" C ASP B 931 " pdb=" N LEU B 932 " ideal model delta sigma weight residual 119.52 113.08 6.44 7.90e-01 1.60e+00 6.64e+01 angle pdb=" C PRO A 943 " pdb=" CA PRO A 943 " pdb=" CB PRO A 943 " ideal model delta sigma weight residual 111.12 101.22 9.90 1.29e+00 6.01e-01 5.89e+01 angle pdb=" N GLN B 935 " pdb=" CA GLN B 935 " pdb=" C GLN B 935 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N ALA A 905 " pdb=" CA ALA A 905 " pdb=" C ALA A 905 " ideal model delta sigma weight residual 110.53 120.11 -9.58 1.32e+00 5.74e-01 5.27e+01 ... (remaining 24099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 9805 15.67 - 31.34: 385 31.34 - 47.01: 91 47.01 - 62.69: 9 62.69 - 78.36: 6 Dihedral angle restraints: 10296 sinusoidal: 3920 harmonic: 6376 Sorted by residual: dihedral pdb=" CA ALA A 903 " pdb=" C ALA A 903 " pdb=" N PRO A 904 " pdb=" CA PRO A 904 " ideal model delta harmonic sigma weight residual 0.00 38.25 -38.25 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" N ASP B 931 " pdb=" C ASP B 931 " pdb=" CA ASP B 931 " pdb=" CB ASP B 931 " ideal model delta harmonic sigma weight residual 122.80 140.33 -17.53 0 2.50e+00 1.60e-01 4.92e+01 dihedral pdb=" C ASP B 931 " pdb=" N ASP B 931 " pdb=" CA ASP B 931 " pdb=" CB ASP B 931 " ideal model delta harmonic sigma weight residual -122.60 -139.49 16.89 0 2.50e+00 1.60e-01 4.56e+01 ... (remaining 10293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2684 0.157 - 0.314: 77 0.314 - 0.471: 7 0.471 - 0.628: 1 0.628 - 0.785: 1 Chirality restraints: 2770 Sorted by residual: chirality pdb=" CA ASP B 931 " pdb=" N ASP B 931 " pdb=" C ASP B 931 " pdb=" CB ASP B 931 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA LYS A1030 " pdb=" N LYS A1030 " pdb=" C LYS A1030 " pdb=" CB LYS A1030 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" CA ILE A 938 " pdb=" N ILE A 938 " pdb=" C ILE A 938 " pdb=" CB ILE A 938 " both_signs ideal model delta sigma weight residual False 2.43 2.89 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 2767 not shown) Planarity restraints: 3074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 929 " -0.027 2.00e-02 2.50e+03 5.50e-02 3.03e+01 pdb=" C ASP B 929 " 0.095 2.00e-02 2.50e+03 pdb=" O ASP B 929 " -0.036 2.00e-02 2.50e+03 pdb=" N ASP B 930 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 943 " -0.020 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C PRO A 943 " 0.073 2.00e-02 2.50e+03 pdb=" O PRO A 943 " -0.029 2.00e-02 2.50e+03 pdb=" N ARG A 944 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1030 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C LYS B1030 " 0.070 2.00e-02 2.50e+03 pdb=" O LYS B1030 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B1031 " -0.025 2.00e-02 2.50e+03 ... (remaining 3071 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2205 2.75 - 3.29: 15342 3.29 - 3.82: 26840 3.82 - 4.36: 32017 4.36 - 4.90: 57203 Nonbonded interactions: 133607 Sorted by model distance: nonbonded pdb=" O THR B 123 " pdb=" OG1 THR B 123 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 63 " pdb=" O GLY A1011 " model vdw 2.216 3.040 nonbonded pdb=" O THR A 123 " pdb=" OG1 THR A 123 " model vdw 2.225 3.040 nonbonded pdb=" O SER B 928 " pdb=" OG SER B 928 " model vdw 2.262 3.040 nonbonded pdb=" O ARG B 870 " pdb=" ND1 HIS B 936 " model vdw 2.304 3.120 ... (remaining 133602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.140 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.722 17602 Z= 0.581 Angle : 1.164 16.190 24108 Z= 0.674 Chirality : 0.071 0.785 2770 Planarity : 0.010 0.072 3074 Dihedral : 9.740 78.358 6190 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.55 % Favored : 92.27 % Rotamer: Outliers : 0.28 % Allowed : 1.79 % Favored : 97.93 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.14), residues: 2224 helix: -2.30 (0.12), residues: 936 sheet: -2.13 (0.32), residues: 232 loop : -3.13 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1062 TYR 0.032 0.004 TYR B1028 PHE 0.044 0.004 PHE B 303 TRP 0.042 0.004 TRP B 636 HIS 0.008 0.002 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.01032 / 0.51 (17598) covalent geometry : angle 1.16373 / 0.67 (24104) SS BOND : bond 0.51064 / 26.87 ( 2) SS BOND : angle 3.37241 / 2.01 ( 4) hydrogen bonds : bond 0.18875 / 13.01 ( 746) hydrogen bonds : angle 6.28166 / 4.35 ( 2121) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 234 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 THR cc_start: 0.8866 (p) cc_final: 0.8631 (t) REVERT: A 847 ARG cc_start: 0.7185 (ttm110) cc_final: 0.6832 (mtt90) REVERT: A 870 ARG cc_start: 0.6632 (ttt180) cc_final: 0.6295 (mtm180) REVERT: A 924 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7411 (ttm170) REVERT: B 28 LEU cc_start: 0.7984 (mp) cc_final: 0.7700 (mp) REVERT: B 110 GLU cc_start: 0.7126 (tt0) cc_final: 0.6737 (tt0) REVERT: B 427 THR cc_start: 0.8892 (p) cc_final: 0.8662 (t) REVERT: B 847 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6783 (mtt90) REVERT: B 870 ARG cc_start: 0.6216 (ttt180) cc_final: 0.5922 (mtm-85) REVERT: B 924 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7384 (ttm170) outliers start: 5 outliers final: 1 residues processed: 238 average time/residue: 0.7284 time to fit residues: 189.5185 Evaluate side-chains 144 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 292 HIS A 604 ASN A 740 GLN A 743 ASN A 885 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 ASN B 146 HIS B 292 HIS B 604 ASN B 723 ASN B 740 GLN B 743 ASN ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 GLN B 936 HIS B1001 ASN C 50 GLN D 50 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114950 restraints weight = 20115.186| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.28 r_work: 0.3180 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17602 Z= 0.130 Angle : 0.622 7.716 24108 Z= 0.318 Chirality : 0.043 0.181 2770 Planarity : 0.006 0.064 3074 Dihedral : 5.843 52.982 2429 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Rotamer: Outliers : 1.18 % Allowed : 8.80 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2224 helix: -0.14 (0.17), residues: 948 sheet: -1.80 (0.32), residues: 252 loop : -2.53 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 139 TYR 0.017 0.002 TYR B 282 PHE 0.016 0.001 PHE A 303 TRP 0.013 0.001 TRP B 342 HIS 0.002 0.000 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (17598) covalent geometry : angle 0.62184 / 0.32 (24104) SS BOND : bond 0.02260 / 1.15 ( 2) SS BOND : angle 1.61915 / 1.35 ( 4) hydrogen bonds : bond 0.05410 / 3.63 ( 746) hydrogen bonds : angle 4.40910 / 3.06 ( 2121) Misc. bond : bond 0.00030 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.483 Fit side-chains REVERT: A 28 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 139 ARG cc_start: 0.7094 (mtm110) cc_final: 0.6736 (mtt90) REVERT: A 427 THR cc_start: 0.8907 (p) cc_final: 0.8667 (t) REVERT: A 552 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7422 (mtt90) REVERT: A 847 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6559 (mtt90) REVERT: A 870 ARG cc_start: 0.7595 (ttt180) cc_final: 0.6432 (mtm180) REVERT: B 28 LEU cc_start: 0.7969 (mp) cc_final: 0.7640 (mp) REVERT: B 110 GLU cc_start: 0.7721 (tt0) cc_final: 0.7317 (tt0) REVERT: B 139 ARG cc_start: 0.7092 (mtm110) cc_final: 0.6704 (mtt90) REVERT: B 427 THR cc_start: 0.8892 (p) cc_final: 0.8668 (t) REVERT: B 552 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7410 (mtt90) REVERT: B 870 ARG cc_start: 0.6993 (ttt180) cc_final: 0.6033 (mtm180) outliers start: 21 outliers final: 6 residues processed: 182 average time/residue: 0.6231 time to fit residues: 126.1004 Evaluate side-chains 147 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 203 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN A 245 HIS A 682 GLN A 710 ASN A 740 GLN A 879 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN B 245 HIS B 710 ASN B 723 ASN B 740 GLN ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN B 935 GLN B 936 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.154592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112890 restraints weight = 20773.249| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.40 r_work: 0.3149 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17602 Z= 0.216 Angle : 0.680 9.127 24108 Z= 0.343 Chirality : 0.046 0.200 2770 Planarity : 0.006 0.056 3074 Dihedral : 5.658 56.999 2428 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 2.41 % Allowed : 9.14 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2224 helix: 0.47 (0.17), residues: 940 sheet: -1.73 (0.33), residues: 240 loop : -2.13 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 401 TYR 0.018 0.002 TYR A 282 PHE 0.026 0.002 PHE A 303 TRP 0.015 0.002 TRP A 343 HIS 0.004 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (17598) covalent geometry : angle 0.68016 / 0.34 (24104) SS BOND : bond 0.00832 / 0.40 ( 2) SS BOND : angle 1.52498 / 1.33 ( 4) hydrogen bonds : bond 0.06567 / 4.45 ( 746) hydrogen bonds : angle 4.29739 / 2.99 ( 2121) Misc. bond : bond 0.00120 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.874 Fit side-chains REVERT: A 28 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 552 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7336 (mtt90) REVERT: A 847 ARG cc_start: 0.6987 (ttm110) cc_final: 0.6639 (mtt90) REVERT: A 870 ARG cc_start: 0.7510 (ttt180) cc_final: 0.6395 (mtm180) REVERT: A 924 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: B 28 LEU cc_start: 0.8001 (mp) cc_final: 0.7678 (mp) REVERT: B 110 GLU cc_start: 0.7757 (tt0) cc_final: 0.7338 (tt0) REVERT: B 139 ARG cc_start: 0.7110 (mtm110) cc_final: 0.6704 (mtt90) REVERT: B 427 THR cc_start: 0.8866 (p) cc_final: 0.8662 (t) REVERT: B 552 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7339 (mtt90) REVERT: B 847 ARG cc_start: 0.7047 (ttm110) cc_final: 0.6680 (mtt90) REVERT: B 870 ARG cc_start: 0.7193 (ttt180) cc_final: 0.6039 (mtm180) REVERT: B 924 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7676 (ttm170) REVERT: B 935 GLN cc_start: 0.5893 (OUTLIER) cc_final: 0.5454 (pp30) outliers start: 43 outliers final: 25 residues processed: 179 average time/residue: 0.7302 time to fit residues: 144.1673 Evaluate side-chains 171 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 769 ASN Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 2 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 156 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** B 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 936 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110909 restraints weight = 20252.428| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.28 r_work: 0.3111 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17602 Z= 0.155 Angle : 0.612 7.800 24108 Z= 0.307 Chirality : 0.043 0.193 2770 Planarity : 0.005 0.053 3074 Dihedral : 5.439 59.810 2428 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 2.02 % Allowed : 10.65 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.18), residues: 2224 helix: 0.82 (0.18), residues: 934 sheet: -1.53 (0.33), residues: 232 loop : -1.96 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 139 TYR 0.016 0.001 TYR B 712 PHE 0.012 0.001 PHE A 303 TRP 0.015 0.001 TRP B 343 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (17598) covalent geometry : angle 0.61184 / 0.31 (24104) SS BOND : bond 0.00756 / 0.38 ( 2) SS BOND : angle 1.49503 / 1.27 ( 4) hydrogen bonds : bond 0.05412 / 3.65 ( 746) hydrogen bonds : angle 4.13535 / 2.88 ( 2121) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.559 Fit side-chains REVERT: A 28 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7699 (mp) REVERT: A 139 ARG cc_start: 0.6960 (mtm110) cc_final: 0.6645 (mtt90) REVERT: A 552 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7302 (mtt90) REVERT: A 847 ARG cc_start: 0.6962 (ttm110) cc_final: 0.6620 (mtt90) REVERT: A 870 ARG cc_start: 0.7426 (ttt180) cc_final: 0.6306 (mtm-85) REVERT: B 28 LEU cc_start: 0.7892 (mp) cc_final: 0.7571 (mp) REVERT: B 110 GLU cc_start: 0.7762 (tt0) cc_final: 0.7351 (tt0) REVERT: B 139 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6601 (mtt90) REVERT: B 552 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7296 (mtt90) REVERT: B 847 ARG cc_start: 0.6987 (ttm110) cc_final: 0.6630 (mtt90) REVERT: B 870 ARG cc_start: 0.7171 (ttt180) cc_final: 0.5975 (mtm180) REVERT: B 935 GLN cc_start: 0.5865 (OUTLIER) cc_final: 0.5119 (pp30) outliers start: 36 outliers final: 18 residues processed: 166 average time/residue: 0.6890 time to fit residues: 126.1402 Evaluate side-chains 154 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 59 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 176 optimal weight: 0.0970 chunk 75 optimal weight: 0.0040 chunk 182 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN B 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114188 restraints weight = 20047.703| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.19 r_work: 0.3167 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17602 Z= 0.106 Angle : 0.559 7.187 24108 Z= 0.278 Chirality : 0.041 0.184 2770 Planarity : 0.005 0.045 3074 Dihedral : 5.082 56.345 2428 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 1.46 % Allowed : 11.77 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 2224 helix: 1.23 (0.18), residues: 924 sheet: -1.29 (0.34), residues: 230 loop : -1.81 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 139 TYR 0.011 0.001 TYR B 712 PHE 0.010 0.001 PHE A 977 TRP 0.012 0.001 TRP B 343 HIS 0.002 0.000 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (17598) covalent geometry : angle 0.55873 / 0.28 (24104) SS BOND : bond 0.00357 / 0.18 ( 2) SS BOND : angle 0.96786 / 0.80 ( 4) hydrogen bonds : bond 0.04184 / 2.81 ( 746) hydrogen bonds : angle 3.89808 / 2.72 ( 2121) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.660 Fit side-chains REVERT: A 24 LEU cc_start: 0.7935 (mt) cc_final: 0.7623 (mm) REVERT: A 28 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7660 (mp) REVERT: A 552 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7242 (mtt90) REVERT: A 847 ARG cc_start: 0.6980 (ttm110) cc_final: 0.6642 (mtt90) REVERT: A 870 ARG cc_start: 0.7415 (ttt180) cc_final: 0.6316 (mtm-85) REVERT: B 28 LEU cc_start: 0.7899 (mp) cc_final: 0.7571 (mp) REVERT: B 110 GLU cc_start: 0.7710 (tt0) cc_final: 0.7289 (tt0) REVERT: B 552 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7241 (mtt90) REVERT: B 847 ARG cc_start: 0.6995 (ttm110) cc_final: 0.6628 (mtt90) REVERT: B 870 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6013 (mtm180) REVERT: B 935 GLN cc_start: 0.5722 (OUTLIER) cc_final: 0.5358 (pp30) outliers start: 26 outliers final: 11 residues processed: 160 average time/residue: 0.7222 time to fit residues: 127.4694 Evaluate side-chains 145 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 0.0060 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 5 optimal weight: 0.0270 chunk 26 optimal weight: 5.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN B 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114710 restraints weight = 19985.584| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.27 r_work: 0.3195 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17602 Z= 0.099 Angle : 0.557 11.325 24108 Z= 0.273 Chirality : 0.041 0.184 2770 Planarity : 0.005 0.043 3074 Dihedral : 4.856 53.180 2428 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 1.57 % Allowed : 12.44 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 2224 helix: 1.40 (0.18), residues: 936 sheet: -1.20 (0.33), residues: 234 loop : -1.71 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 171 TYR 0.011 0.001 TYR A1007 PHE 0.010 0.001 PHE B 977 TRP 0.011 0.001 TRP B 343 HIS 0.003 0.000 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (17598) covalent geometry : angle 0.55679 / 0.27 (24104) SS BOND : bond 0.00298 / 0.15 ( 2) SS BOND : angle 0.68217 / 0.56 ( 4) hydrogen bonds : bond 0.03804 / 2.55 ( 746) hydrogen bonds : angle 3.76513 / 2.63 ( 2121) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.643 Fit side-chains REVERT: A 24 LEU cc_start: 0.7885 (mt) cc_final: 0.7575 (mm) REVERT: A 28 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7638 (mp) REVERT: A 171 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7589 (mtp-110) REVERT: A 552 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7285 (mtt90) REVERT: A 820 ARG cc_start: 0.6587 (mpp-170) cc_final: 0.6299 (mpt90) REVERT: A 847 ARG cc_start: 0.6933 (ttm110) cc_final: 0.6586 (mtt90) REVERT: A 870 ARG cc_start: 0.7366 (ttt180) cc_final: 0.6260 (mtm-85) REVERT: B 28 LEU cc_start: 0.7892 (mp) cc_final: 0.7534 (mp) REVERT: B 110 GLU cc_start: 0.7674 (tt0) cc_final: 0.7228 (tt0) REVERT: B 552 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7251 (mtt90) REVERT: B 847 ARG cc_start: 0.6966 (ttm110) cc_final: 0.6614 (mtt90) REVERT: B 870 ARG cc_start: 0.7166 (ttt180) cc_final: 0.5980 (mtm180) REVERT: B 935 GLN cc_start: 0.5917 (OUTLIER) cc_final: 0.5608 (pp30) outliers start: 28 outliers final: 17 residues processed: 163 average time/residue: 0.6830 time to fit residues: 122.7230 Evaluate side-chains 157 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 552 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 206 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 199 optimal weight: 0.0020 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115470 restraints weight = 19941.249| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.24 r_work: 0.3208 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17602 Z= 0.100 Angle : 0.549 10.469 24108 Z= 0.269 Chirality : 0.041 0.185 2770 Planarity : 0.005 0.043 3074 Dihedral : 4.699 48.453 2428 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 1.68 % Allowed : 12.44 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 2224 helix: 1.46 (0.18), residues: 950 sheet: -0.96 (0.34), residues: 230 loop : -1.69 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 171 TYR 0.012 0.001 TYR A1007 PHE 0.010 0.001 PHE A 977 TRP 0.010 0.001 TRP B 343 HIS 0.003 0.000 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (17598) covalent geometry : angle 0.54899 / 0.27 (24104) SS BOND : bond 0.00367 / 0.18 ( 2) SS BOND : angle 0.89067 / 0.74 ( 4) hydrogen bonds : bond 0.03750 / 2.52 ( 746) hydrogen bonds : angle 3.69031 / 2.57 ( 2121) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.576 Fit side-chains REVERT: A 24 LEU cc_start: 0.7910 (mt) cc_final: 0.7602 (mm) REVERT: A 28 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7672 (mp) REVERT: A 171 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7553 (mtp-110) REVERT: A 847 ARG cc_start: 0.6953 (ttm110) cc_final: 0.6603 (mtt90) REVERT: A 870 ARG cc_start: 0.7375 (ttt180) cc_final: 0.6309 (mtm-85) REVERT: B 28 LEU cc_start: 0.7924 (mp) cc_final: 0.7573 (mp) REVERT: B 110 GLU cc_start: 0.7637 (tt0) cc_final: 0.7231 (tt0) REVERT: B 173 GLU cc_start: 0.7600 (mp0) cc_final: 0.7310 (mp0) REVERT: B 847 ARG cc_start: 0.6978 (ttm110) cc_final: 0.6627 (mtt90) REVERT: B 870 ARG cc_start: 0.7208 (ttt180) cc_final: 0.6083 (mtm180) outliers start: 30 outliers final: 18 residues processed: 158 average time/residue: 0.6832 time to fit residues: 119.0939 Evaluate side-chains 153 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 105 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111476 restraints weight = 19998.821| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.30 r_work: 0.3153 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17602 Z= 0.133 Angle : 0.584 9.417 24108 Z= 0.288 Chirality : 0.042 0.188 2770 Planarity : 0.005 0.044 3074 Dihedral : 4.758 41.440 2428 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.39 % Rotamer: Outliers : 1.35 % Allowed : 13.34 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 2224 helix: 1.42 (0.18), residues: 944 sheet: -1.02 (0.34), residues: 232 loop : -1.57 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 171 TYR 0.014 0.001 TYR A 712 PHE 0.010 0.001 PHE B 977 TRP 0.011 0.001 TRP B 343 HIS 0.003 0.001 HIS B 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (17598) covalent geometry : angle 0.58347 / 0.29 (24104) SS BOND : bond 0.00676 / 0.34 ( 2) SS BOND : angle 1.07203 / 0.90 ( 4) hydrogen bonds : bond 0.04708 / 3.18 ( 746) hydrogen bonds : angle 3.81174 / 2.65 ( 2121) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7923 (mt) cc_final: 0.7626 (mm) REVERT: A 28 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 110 GLU cc_start: 0.8331 (pm20) cc_final: 0.7300 (pm20) REVERT: A 847 ARG cc_start: 0.6991 (ttm110) cc_final: 0.6629 (mtt90) REVERT: A 870 ARG cc_start: 0.7364 (ttt180) cc_final: 0.6246 (mtm-85) REVERT: A 935 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.6142 (pp30) REVERT: B 28 LEU cc_start: 0.7965 (mp) cc_final: 0.7632 (mp) REVERT: B 110 GLU cc_start: 0.7699 (tt0) cc_final: 0.7292 (tt0) REVERT: B 847 ARG cc_start: 0.7026 (ttm110) cc_final: 0.6663 (mtt90) REVERT: B 870 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6041 (mtm180) outliers start: 24 outliers final: 16 residues processed: 147 average time/residue: 0.7138 time to fit residues: 116.2536 Evaluate side-chains 147 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 33 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN B 769 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113598 restraints weight = 20112.151| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.30 r_work: 0.3164 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17602 Z= 0.114 Angle : 0.565 9.034 24108 Z= 0.278 Chirality : 0.041 0.186 2770 Planarity : 0.005 0.044 3074 Dihedral : 4.667 37.491 2428 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 1.23 % Allowed : 13.68 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 2224 helix: 1.51 (0.18), residues: 944 sheet: -0.93 (0.33), residues: 230 loop : -1.57 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 171 TYR 0.014 0.001 TYR B1007 PHE 0.010 0.001 PHE A 977 TRP 0.014 0.001 TRP B 343 HIS 0.009 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (17598) covalent geometry : angle 0.56507 / 0.28 (24104) SS BOND : bond 0.00502 / 0.25 ( 2) SS BOND : angle 0.96553 / 0.80 ( 4) hydrogen bonds : bond 0.04254 / 2.86 ( 746) hydrogen bonds : angle 3.75004 / 2.61 ( 2121) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.657 Fit side-chains REVERT: A 24 LEU cc_start: 0.7938 (mt) cc_final: 0.7620 (mm) REVERT: A 28 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7669 (mp) REVERT: A 110 GLU cc_start: 0.8341 (pm20) cc_final: 0.8135 (pm20) REVERT: A 171 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7349 (mtp-110) REVERT: A 847 ARG cc_start: 0.6970 (ttm110) cc_final: 0.6609 (mtt90) REVERT: A 870 ARG cc_start: 0.7409 (ttt180) cc_final: 0.6268 (mtm-85) REVERT: B 24 LEU cc_start: 0.7924 (mt) cc_final: 0.7546 (mm) REVERT: B 28 LEU cc_start: 0.7934 (mp) cc_final: 0.7578 (mp) REVERT: B 110 GLU cc_start: 0.7692 (tt0) cc_final: 0.7326 (tt0) REVERT: B 847 ARG cc_start: 0.7003 (ttm110) cc_final: 0.6645 (mtt90) REVERT: B 870 ARG cc_start: 0.7171 (ttt180) cc_final: 0.6031 (mtm180) outliers start: 22 outliers final: 15 residues processed: 148 average time/residue: 0.7223 time to fit residues: 118.3668 Evaluate side-chains 147 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 16 ARG Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114433 restraints weight = 19978.075| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.34 r_work: 0.3198 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17602 Z= 0.103 Angle : 0.555 9.077 24108 Z= 0.272 Chirality : 0.041 0.183 2770 Planarity : 0.005 0.044 3074 Dihedral : 4.510 30.929 2428 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.12 % Allowed : 13.73 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 2224 helix: 1.62 (0.18), residues: 944 sheet: -0.81 (0.34), residues: 230 loop : -1.55 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 139 TYR 0.015 0.001 TYR B1007 PHE 0.009 0.001 PHE A 977 TRP 0.012 0.001 TRP B 343 HIS 0.003 0.000 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (17598) covalent geometry : angle 0.55506 / 0.27 (24104) SS BOND : bond 0.00348 / 0.17 ( 2) SS BOND : angle 0.82226 / 0.69 ( 4) hydrogen bonds : bond 0.03795 / 2.54 ( 746) hydrogen bonds : angle 3.66954 / 2.55 ( 2121) Misc. bond : bond 0.00025 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4448 Ramachandran restraints generated. 2224 Oldfield, 0 Emsley, 2224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.677 Fit side-chains REVERT: A 24 LEU cc_start: 0.7927 (mt) cc_final: 0.7616 (mm) REVERT: A 28 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 139 ARG cc_start: 0.6885 (mtm110) cc_final: 0.6615 (mtt90) REVERT: A 151 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7558 (m) REVERT: A 847 ARG cc_start: 0.6990 (ttm110) cc_final: 0.6644 (mtt90) REVERT: A 870 ARG cc_start: 0.7397 (ttt180) cc_final: 0.6309 (mtm-85) REVERT: A 935 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.6093 (pp30) REVERT: B 24 LEU cc_start: 0.7937 (mt) cc_final: 0.7564 (mm) REVERT: B 28 LEU cc_start: 0.7948 (mp) cc_final: 0.7605 (mp) REVERT: B 110 GLU cc_start: 0.7643 (tt0) cc_final: 0.7307 (tt0) REVERT: B 847 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6679 (mtt90) REVERT: B 870 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6062 (mtm180) outliers start: 20 outliers final: 15 residues processed: 144 average time/residue: 0.7085 time to fit residues: 112.9664 Evaluate side-chains 147 residues out of total 1786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1007 TYR Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1007 TYR Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 113 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.158598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114133 restraints weight = 19939.445| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.31 r_work: 0.3195 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17602 Z= 0.108 Angle : 0.558 8.893 24108 Z= 0.274 Chirality : 0.041 0.184 2770 Planarity : 0.005 0.058 3074 Dihedral : 4.484 28.661 2428 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.07 % Allowed : 13.85 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 2224 helix: 1.62 (0.18), residues: 944 sheet: -0.80 (0.34), residues: 230 loop : -1.53 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 139 TYR 0.015 0.001 TYR B1007 PHE 0.009 0.001 PHE A 977 TRP 0.012 0.001 TRP B 343 HIS 0.003 0.001 HIS B 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (17598) covalent geometry : angle 0.55806 / 0.27 (24104) SS BOND : bond 0.00450 / 0.23 ( 2) SS BOND : angle 0.86694 / 0.73 ( 4) hydrogen bonds : bond 0.03911 / 2.63 ( 746) hydrogen bonds : angle 3.67072 / 2.56 ( 2121) Misc. bond : bond 0.00029 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5740.02 seconds wall clock time: 98 minutes 14.10 seconds (5894.10 seconds total)