Starting phenix.real_space_refine on Sat Aug 8 05:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjq_65119/08_2026/9vjq_65119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjq_65119/08_2026/9vjq_65119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vjq_65119/08_2026/9vjq_65119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjq_65119/08_2026/9vjq_65119.map" model { file = "/net/cci-nas-00/data/ceres_data/9vjq_65119/08_2026/9vjq_65119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjq_65119/08_2026/9vjq_65119.cif" } resolution = 2.9 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= 0.003 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 4 9.91 5 P 12 5.49 5 S 100 5.16 5 C 16532 2.51 5 N 4112 2.21 5 O 4548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25308 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6268 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 764} Chain breaks: 18 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 6268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6268 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 764} Chain breaks: 18 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 6268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6268 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 764} Chain breaks: 18 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 6268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6268 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 764} Chain breaks: 18 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' CA': 1, 'PIO': 1, 'XUQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' CA': 1, 'PIO': 1, 'XUQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' CA': 1, 'PIO': 1, 'XUQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' CA': 1, 'PIO': 1, 'XUQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.24, per 1000 atoms: 0.17 Number of scatterers: 25308 At special positions: 0 Unit cell: (149.792, 149.792, 143.994, 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 4 19.99 S 100 16.00 P 12 15.00 O 4548 8.00 N 4112 7.00 C 16532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 927.1 milliseconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5984 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 8 sheets defined 75.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 removed outlier: 4.459A pdb=" N HIS A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 removed outlier: 3.579A pdb=" N ILE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.596A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.652A pdb=" N ARG A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.860A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 387 removed outlier: 4.122A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 removed outlier: 3.778A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.525A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.672A pdb=" N PHE A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.730A pdb=" N TYR A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.795A pdb=" N THR A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.648A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.689A pdb=" N LYS A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 612 through 636 removed outlier: 3.980A pdb=" N GLU A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.890A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.749A pdb=" N GLY A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 663 removed outlier: 3.640A pdb=" N ALA A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 768 through 788 removed outlier: 4.097A pdb=" N TYR A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 784 " --> pdb=" O CYS A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.509A pdb=" N THR A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 813 removed outlier: 4.082A pdb=" N TYR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA A 811 " --> pdb=" O PHE A 807 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 4.216A pdb=" N ILE A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 832 " --> pdb=" O GLY A 828 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 836 " --> pdb=" O PHE A 832 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 837 " --> pdb=" O CYS A 833 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 850 removed outlier: 3.508A pdb=" N HIS A 845 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 847 " --> pdb=" O ILE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 890 removed outlier: 4.097A pdb=" N ILE A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 987 removed outlier: 3.516A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 970 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 982 " --> pdb=" O MET A 978 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 removed outlier: 4.038A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.943A pdb=" N VAL A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1068 Processing helix chain 'A' and resid 1075 through 1104 Processing helix chain 'D' and resid 125 through 136 removed outlier: 4.459A pdb=" N HIS D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 removed outlier: 3.577A pdb=" N ILE D 169 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.611A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 removed outlier: 3.664A pdb=" N ARG D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 removed outlier: 3.859A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 387 removed outlier: 4.125A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 removed outlier: 3.783A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 437 removed outlier: 3.514A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 458 through 468 removed outlier: 3.666A pdb=" N PHE D 463 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 removed outlier: 3.734A pdb=" N TYR D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 507 " --> pdb=" O THR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.784A pdb=" N THR D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.652A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.692A pdb=" N LYS D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 612 through 636 removed outlier: 3.982A pdb=" N GLU D 616 " --> pdb=" O GLY D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 648 through 652 removed outlier: 3.753A pdb=" N GLY D 652 " --> pdb=" O GLU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.632A pdb=" N ALA D 663 " --> pdb=" O LEU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 768 through 788 removed outlier: 4.095A pdb=" N TYR D 772 " --> pdb=" O GLU D 768 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 778 " --> pdb=" O LEU D 774 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 784 " --> pdb=" O CYS D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 795 removed outlier: 3.516A pdb=" N THR D 795 " --> pdb=" O VAL D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 813 removed outlier: 4.083A pdb=" N TYR D 808 " --> pdb=" O LEU D 804 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE D 809 " --> pdb=" O GLY D 805 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA D 811 " --> pdb=" O PHE D 807 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 813 " --> pdb=" O PHE D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 840 removed outlier: 4.215A pdb=" N ILE D 831 " --> pdb=" O SER D 827 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR D 836 " --> pdb=" O PHE D 832 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE D 837 " --> pdb=" O CYS D 833 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 850 removed outlier: 3.507A pdb=" N HIS D 845 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 846 " --> pdb=" O LEU D 843 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 847 " --> pdb=" O ILE D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 890 removed outlier: 4.094A pdb=" N ILE D 857 " --> pdb=" O LEU D 853 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE D 865 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP D 866 " --> pdb=" O ARG D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 987 removed outlier: 3.517A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU D 970 " --> pdb=" O SER D 966 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 981 " --> pdb=" O ALA D 977 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 982 " --> pdb=" O MET D 978 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 983 " --> pdb=" O PHE D 979 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 984 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 985 " --> pdb=" O TYR D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1008 removed outlier: 4.035A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D1002 " --> pdb=" O ARG D 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1017 removed outlier: 3.898A pdb=" N VAL D1017 " --> pdb=" O PHE D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1068 Processing helix chain 'D' and resid 1075 through 1104 Processing helix chain 'B' and resid 125 through 136 removed outlier: 4.460A pdb=" N HIS B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.577A pdb=" N ILE B 169 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.610A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.664A pdb=" N ARG B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 removed outlier: 3.860A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 removed outlier: 4.126A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 removed outlier: 3.782A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 437 removed outlier: 3.513A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.651A pdb=" N PHE B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.734A pdb=" N TYR B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 533 removed outlier: 3.790A pdb=" N THR B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.650A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.685A pdb=" N LYS B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 612 through 636 removed outlier: 3.981A pdb=" N GLU B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.752A pdb=" N GLY B 652 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.633A pdb=" N ALA B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 768 through 788 removed outlier: 4.095A pdb=" N TYR B 772 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 778 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 784 " --> pdb=" O CYS B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 795 removed outlier: 3.515A pdb=" N THR B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 813 removed outlier: 4.083A pdb=" N TYR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 809 " --> pdb=" O GLY B 805 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA B 811 " --> pdb=" O PHE B 807 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 813 " --> pdb=" O PHE B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 840 removed outlier: 4.216A pdb=" N ILE B 831 " --> pdb=" O SER B 827 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 832 " --> pdb=" O GLY B 828 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 837 " --> pdb=" O CYS B 833 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 850 removed outlier: 3.508A pdb=" N HIS B 845 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 846 " --> pdb=" O LEU B 843 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 890 removed outlier: 4.094A pdb=" N ILE B 857 " --> pdb=" O LEU B 853 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP B 866 " --> pdb=" O ARG B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 987 removed outlier: 3.516A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 982 " --> pdb=" O MET B 978 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 983 " --> pdb=" O PHE B 979 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 984 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 985 " --> pdb=" O TYR B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1008 removed outlier: 4.034A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B1002 " --> pdb=" O ARG B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.899A pdb=" N VAL B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1068 Processing helix chain 'B' and resid 1075 through 1104 Processing helix chain 'C' and resid 125 through 136 removed outlier: 4.458A pdb=" N HIS C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 removed outlier: 3.577A pdb=" N ILE C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 removed outlier: 3.612A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.664A pdb=" N ARG C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.860A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 387 removed outlier: 4.126A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 removed outlier: 3.782A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 437 removed outlier: 3.512A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.652A pdb=" N PHE C 463 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.734A pdb=" N TYR C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.785A pdb=" N THR C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.650A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 removed outlier: 3.684A pdb=" N LYS C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 612 through 636 removed outlier: 3.981A pdb=" N GLU C 616 " --> pdb=" O GLY C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.752A pdb=" N GLY C 652 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.629A pdb=" N ALA C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 724 through 732 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 768 through 788 removed outlier: 4.095A pdb=" N TYR C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 778 " --> pdb=" O LEU C 774 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 784 " --> pdb=" O CYS C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 795 removed outlier: 3.515A pdb=" N THR C 795 " --> pdb=" O VAL C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 813 removed outlier: 4.083A pdb=" N TYR C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA C 811 " --> pdb=" O PHE C 807 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 813 " --> pdb=" O PHE C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 840 removed outlier: 4.215A pdb=" N ILE C 831 " --> pdb=" O SER C 827 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 832 " --> pdb=" O GLY C 828 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR C 836 " --> pdb=" O PHE C 832 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE C 837 " --> pdb=" O CYS C 833 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 850 removed outlier: 3.527A pdb=" N HIS C 845 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 846 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 847 " --> pdb=" O ILE C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 890 removed outlier: 4.095A pdb=" N ILE C 857 " --> pdb=" O LEU C 853 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP C 866 " --> pdb=" O ARG C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 987 removed outlier: 3.512A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU C 970 " --> pdb=" O SER C 966 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 982 " --> pdb=" O MET C 978 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 983 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 984 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 985 " --> pdb=" O TYR C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1008 removed outlier: 4.037A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C1002 " --> pdb=" O ARG C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1017 removed outlier: 3.899A pdb=" N VAL C1017 " --> pdb=" O PHE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1068 Processing helix chain 'C' and resid 1075 through 1104 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.684A pdb=" N HIS A 259 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 210 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN A 143 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU A 180 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 145 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AA4, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.693A pdb=" N HIS D 259 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL D 210 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN D 143 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU D 180 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 260 removed outlier: 3.692A pdb=" N HIS B 259 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 210 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B 143 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU B 180 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 145 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.690A pdb=" N HIS C 259 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 210 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ASN C 143 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU C 180 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 145 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) 1536 hydrogen bonds defined for protein. 4536 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: 4.52 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4028 1.31 - 1.43: 7106 1.43 - 1.56: 14498 1.56 - 1.68: 16 1.68 - 1.81: 156 Bond restraints: 25804 Sorted by residual: bond pdb=" C1B PIO B1201 " pdb=" O3C PIO B1201 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1B PIO D1201 " pdb=" O3C PIO D1201 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1B PIO C1201 " pdb=" O3C PIO C1201 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1A PIO D1201 " pdb=" O2C PIO D1201 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1A PIO C1201 " pdb=" O2C PIO C1201 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 25799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 34558 2.31 - 4.62: 331 4.62 - 6.93: 51 6.93 - 9.24: 8 9.24 - 11.55: 12 Bond angle restraints: 34960 Sorted by residual: angle pdb=" O11 PIO A1201 " pdb=" P1 PIO A1201 " pdb=" O12 PIO A1201 " ideal model delta sigma weight residual 121.09 109.54 11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" O11 PIO C1201 " pdb=" P1 PIO C1201 " pdb=" O12 PIO C1201 " ideal model delta sigma weight residual 121.09 109.55 11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" O11 PIO B1201 " pdb=" P1 PIO B1201 " pdb=" O12 PIO B1201 " ideal model delta sigma weight residual 121.09 109.56 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" O11 PIO D1201 " pdb=" P1 PIO D1201 " pdb=" O12 PIO D1201 " ideal model delta sigma weight residual 121.09 109.58 11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O1 PIO A1201 " pdb=" P1 PIO A1201 " pdb=" O13 PIO A1201 " ideal model delta sigma weight residual 97.64 109.01 -11.37 3.00e+00 1.11e-01 1.44e+01 ... (remaining 34955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 13332 21.81 - 43.62: 1414 43.62 - 65.42: 326 65.42 - 87.23: 40 87.23 - 109.04: 12 Dihedral angle restraints: 15124 sinusoidal: 5972 harmonic: 9152 Sorted by residual: dihedral pdb=" C23 XUQ B1203 " pdb=" C33 XUQ B1203 " pdb=" C43 XUQ B1203 " pdb=" C53 XUQ B1203 " ideal model delta sinusoidal sigma weight residual 57.04 -52.00 109.04 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C23 XUQ C1203 " pdb=" C33 XUQ C1203 " pdb=" C43 XUQ C1203 " pdb=" C53 XUQ C1203 " ideal model delta sinusoidal sigma weight residual 57.04 -51.94 108.98 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C23 XUQ D1203 " pdb=" C33 XUQ D1203 " pdb=" C43 XUQ D1203 " pdb=" C53 XUQ D1203 " ideal model delta sinusoidal sigma weight residual 57.04 -51.93 108.97 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 15121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3455 0.048 - 0.095: 519 0.095 - 0.143: 82 0.143 - 0.190: 0 0.190 - 0.238: 4 Chirality restraints: 4060 Sorted by residual: chirality pdb=" C13 XUQ C1203 " pdb=" C23 XUQ C1203 " pdb=" C63 XUQ C1203 " pdb=" O13 XUQ C1203 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C13 XUQ A1203 " pdb=" C23 XUQ A1203 " pdb=" C63 XUQ A1203 " pdb=" O13 XUQ A1203 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C13 XUQ B1203 " pdb=" C23 XUQ B1203 " pdb=" C63 XUQ B1203 " pdb=" O13 XUQ B1203 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4057 not shown) Planarity restraints: 4260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 141 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO C 142 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 141 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 142 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 141 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 142 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.027 5.00e-02 4.00e+02 ... (remaining 4257 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 9536 2.89 - 3.39: 24575 3.39 - 3.89: 38946 3.89 - 4.40: 43928 4.40 - 4.90: 75465 Nonbonded interactions: 192450 Sorted by model distance: nonbonded pdb=" O THR D 141 " pdb=" OG1 THR D 141 " model vdw 2.384 3.040 nonbonded pdb=" O THR B 141 " pdb=" OG1 THR B 141 " model vdw 2.384 3.040 nonbonded pdb=" O THR C 141 " pdb=" OG1 THR C 141 " model vdw 2.385 3.040 nonbonded pdb=" O THR A 141 " pdb=" OG1 THR A 141 " model vdw 2.386 3.040 nonbonded pdb=" O GLU B 420 " pdb=" OE1 GLU B 420 " model vdw 2.445 3.040 ... (remaining 192445 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.003 0.068 25804 Z= 0.147 Angle : 0.599 11.547 34960 Z= 0.302 Chirality : 0.035 0.238 4060 Planarity : 0.003 0.048 4260 Dihedral : 18.413 109.038 9140 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.17 % Allowed : 27.44 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2964 helix: 1.10 (0.12), residues: 2188 sheet: -2.78 (0.37), residues: 124 loop : -1.69 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 197 TYR 0.010 0.001 TYR D 191 PHE 0.011 0.001 PHE A1015 TRP 0.015 0.001 TRP A 453 HIS 0.003 0.001 HIS D 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (25804) covalent geometry : angle 0.59912 / 0.30 (34960) hydrogen bonds : bond 0.16244 / 10.54 ( 1536) hydrogen bonds : angle 5.60618 / 4.00 ( 4536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 310 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6993 (mtp85) cc_final: 0.6532 (mtm-85) REVERT: A 199 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7522 (t0) REVERT: A 253 LEU cc_start: 0.7742 (mt) cc_final: 0.7058 (pp) REVERT: A 861 GLN cc_start: 0.7877 (mt0) cc_final: 0.7658 (mt0) REVERT: A 1066 LYS cc_start: 0.7219 (mttm) cc_final: 0.7008 (mtpm) REVERT: D 162 ARG cc_start: 0.7022 (mtp85) cc_final: 0.6528 (mtm-85) REVERT: D 199 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7592 (t0) REVERT: D 253 LEU cc_start: 0.7757 (mt) cc_final: 0.7055 (pp) REVERT: B 162 ARG cc_start: 0.7023 (mtp85) cc_final: 0.6537 (mtm-85) REVERT: B 199 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7571 (t0) REVERT: B 253 LEU cc_start: 0.7754 (mt) cc_final: 0.7057 (pp) REVERT: C 162 ARG cc_start: 0.7045 (mtp85) cc_final: 0.6559 (mtm-85) REVERT: C 199 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7604 (t0) REVERT: C 253 LEU cc_start: 0.7750 (mt) cc_final: 0.7042 (pp) REVERT: C 861 GLN cc_start: 0.7926 (mt0) cc_final: 0.7713 (mt0) outliers start: 31 outliers final: 23 residues processed: 329 average time/residue: 0.4849 time to fit residues: 192.3724 Evaluate side-chains 324 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 845 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 317 ASN A 619 ASN D 317 ASN D 438 GLN D 483 ASN D 619 ASN D1007 ASN B 317 ASN B 438 GLN B 619 ASN B1007 ASN C 256 ASN C 317 ASN C 438 GLN C 619 ASN C1007 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.202306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128308 restraints weight = 29728.004| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.25 r_work: 0.3313 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25804 Z= 0.158 Angle : 0.539 7.030 34960 Z= 0.276 Chirality : 0.039 0.144 4060 Planarity : 0.004 0.054 4260 Dihedral : 7.865 77.095 3475 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.59 % Allowed : 23.20 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.15), residues: 2964 helix: 1.28 (0.11), residues: 2216 sheet: -2.40 (0.40), residues: 124 loop : -1.98 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.012 0.002 TYR D 621 PHE 0.017 0.002 PHE D 752 TRP 0.013 0.001 TRP A 426 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (25804) covalent geometry : angle 0.53936 / 0.28 (34960) hydrogen bonds : bond 0.05531 / 3.61 ( 1536) hydrogen bonds : angle 4.04237 / 2.89 ( 4536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 329 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6763 (mtp85) cc_final: 0.6214 (mtm-85) REVERT: A 181 THR cc_start: 0.6952 (m) cc_final: 0.6667 (p) REVERT: A 199 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7350 (t0) REVERT: A 620 GLU cc_start: 0.8220 (tt0) cc_final: 0.7451 (mt-10) REVERT: A 780 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7636 (p) REVERT: A 861 GLN cc_start: 0.7490 (mt0) cc_final: 0.7200 (mt0) REVERT: D 162 ARG cc_start: 0.6818 (mtp85) cc_final: 0.6256 (mtm-85) REVERT: D 181 THR cc_start: 0.6961 (m) cc_final: 0.6664 (p) REVERT: D 242 MET cc_start: 0.5475 (ptm) cc_final: 0.5158 (ppp) REVERT: D 486 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8307 (mtmt) REVERT: D 620 GLU cc_start: 0.8237 (tt0) cc_final: 0.7463 (mt-10) REVERT: D 780 CYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7669 (p) REVERT: D 861 GLN cc_start: 0.7481 (mt0) cc_final: 0.7193 (mt0) REVERT: B 162 ARG cc_start: 0.6806 (mtp85) cc_final: 0.6243 (mtm-85) REVERT: B 181 THR cc_start: 0.6961 (m) cc_final: 0.6663 (p) REVERT: B 242 MET cc_start: 0.5485 (ptm) cc_final: 0.5169 (ppp) REVERT: B 620 GLU cc_start: 0.8229 (tt0) cc_final: 0.7461 (mt-10) REVERT: B 780 CYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7661 (p) REVERT: B 861 GLN cc_start: 0.7476 (mt0) cc_final: 0.7186 (mt0) REVERT: C 162 ARG cc_start: 0.6800 (mtp85) cc_final: 0.6241 (mtm-85) REVERT: C 181 THR cc_start: 0.6962 (m) cc_final: 0.6665 (p) REVERT: C 242 MET cc_start: 0.5485 (ptm) cc_final: 0.5172 (ppp) REVERT: C 620 GLU cc_start: 0.8229 (tt0) cc_final: 0.7465 (mt-10) REVERT: C 780 CYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7667 (p) REVERT: C 861 GLN cc_start: 0.7483 (mt0) cc_final: 0.7189 (mt0) outliers start: 122 outliers final: 52 residues processed: 419 average time/residue: 0.4864 time to fit residues: 247.0045 Evaluate side-chains 369 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 780 CYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 518 ASP Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 876 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 88 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 0.0060 chunk 192 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.210514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135490 restraints weight = 29530.615| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.33 r_work: 0.3328 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 25804 Z= 0.106 Angle : 0.466 6.980 34960 Z= 0.238 Chirality : 0.036 0.160 4060 Planarity : 0.003 0.048 4260 Dihedral : 5.829 49.286 3458 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.12 % Allowed : 25.49 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.16), residues: 2964 helix: 1.50 (0.11), residues: 2216 sheet: -1.95 (0.43), residues: 124 loop : -1.92 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 167 TYR 0.016 0.001 TYR D 191 PHE 0.019 0.001 PHE B 752 TRP 0.012 0.001 TRP A 426 HIS 0.002 0.000 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (25804) covalent geometry : angle 0.46609 / 0.24 (34960) hydrogen bonds : bond 0.04270 / 2.78 ( 1536) hydrogen bonds : angle 3.67253 / 2.62 ( 4536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 322 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6693 (mtp85) cc_final: 0.6186 (mtm-85) REVERT: A 181 THR cc_start: 0.6880 (m) cc_final: 0.6599 (p) REVERT: A 321 LYS cc_start: 0.7881 (tptm) cc_final: 0.7614 (mmmt) REVERT: A 620 GLU cc_start: 0.8219 (tt0) cc_final: 0.7409 (mt-10) REVERT: A 631 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: D 162 ARG cc_start: 0.6701 (mtp85) cc_final: 0.6179 (mtm-85) REVERT: D 181 THR cc_start: 0.6880 (m) cc_final: 0.6556 (p) REVERT: D 620 GLU cc_start: 0.8227 (tt0) cc_final: 0.7416 (mt-10) REVERT: D 631 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: B 162 ARG cc_start: 0.6782 (mtp85) cc_final: 0.6265 (mtm-85) REVERT: B 181 THR cc_start: 0.6885 (m) cc_final: 0.6561 (p) REVERT: B 620 GLU cc_start: 0.8217 (tt0) cc_final: 0.7406 (mt-10) REVERT: B 631 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: C 162 ARG cc_start: 0.6759 (mtp85) cc_final: 0.6241 (mtm-85) REVERT: C 181 THR cc_start: 0.6901 (m) cc_final: 0.6575 (p) REVERT: C 620 GLU cc_start: 0.8218 (tt0) cc_final: 0.7410 (mt-10) REVERT: C 631 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: C 842 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5981 (tpp-160) REVERT: C 845 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7699 (p-80) outliers start: 83 outliers final: 36 residues processed: 388 average time/residue: 0.4775 time to fit residues: 225.9439 Evaluate side-chains 326 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 867 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 226 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 0.4980 chunk 197 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133852 restraints weight = 29463.223| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.34 r_work: 0.3304 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25804 Z= 0.126 Angle : 0.489 9.465 34960 Z= 0.249 Chirality : 0.037 0.139 4060 Planarity : 0.004 0.051 4260 Dihedral : 5.590 46.012 3450 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.02 % Allowed : 25.26 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.16), residues: 2964 helix: 1.54 (0.11), residues: 2212 sheet: -1.92 (0.38), residues: 156 loop : -2.01 (0.21), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.015 0.001 TYR B 191 PHE 0.021 0.001 PHE B 752 TRP 0.011 0.001 TRP D 740 HIS 0.003 0.001 HIS B 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (25804) covalent geometry : angle 0.48900 / 0.25 (34960) hydrogen bonds : bond 0.04523 / 2.96 ( 1536) hydrogen bonds : angle 3.60153 / 2.58 ( 4536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 301 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6712 (mtp85) cc_final: 0.6193 (mtm-85) REVERT: A 181 THR cc_start: 0.7078 (m) cc_final: 0.6785 (p) REVERT: A 321 LYS cc_start: 0.7930 (tptm) cc_final: 0.7656 (mmmt) REVERT: A 620 GLU cc_start: 0.8257 (tt0) cc_final: 0.7482 (mt-10) REVERT: A 842 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5993 (tpp-160) REVERT: D 162 ARG cc_start: 0.6717 (mtp85) cc_final: 0.6215 (mtm-85) REVERT: D 181 THR cc_start: 0.7052 (m) cc_final: 0.6751 (p) REVERT: D 620 GLU cc_start: 0.8268 (tt0) cc_final: 0.7494 (mt-10) REVERT: D 631 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: D 842 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5940 (tpp-160) REVERT: B 162 ARG cc_start: 0.6715 (mtp85) cc_final: 0.6192 (mtm-85) REVERT: B 181 THR cc_start: 0.7044 (m) cc_final: 0.6745 (p) REVERT: B 620 GLU cc_start: 0.8259 (tt0) cc_final: 0.7480 (mt-10) REVERT: B 631 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 842 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5999 (tpp-160) REVERT: C 162 ARG cc_start: 0.6702 (mtp85) cc_final: 0.6184 (mtm-85) REVERT: C 181 THR cc_start: 0.7071 (m) cc_final: 0.6770 (p) REVERT: C 620 GLU cc_start: 0.8260 (tt0) cc_final: 0.7487 (mt-10) REVERT: C 631 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: C 842 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6012 (tpp-160) outliers start: 107 outliers final: 43 residues processed: 375 average time/residue: 0.5075 time to fit residues: 228.9993 Evaluate side-chains 343 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 224 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 299 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.207886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132240 restraints weight = 29318.467| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.33 r_work: 0.3270 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25804 Z= 0.171 Angle : 0.528 7.989 34960 Z= 0.271 Chirality : 0.038 0.147 4060 Planarity : 0.004 0.055 4260 Dihedral : 5.226 44.992 3440 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.06 % Allowed : 25.71 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.15), residues: 2964 helix: 1.46 (0.11), residues: 2188 sheet: -1.94 (0.38), residues: 156 loop : -2.11 (0.20), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 310 TYR 0.016 0.001 TYR D 191 PHE 0.022 0.002 PHE B 752 TRP 0.014 0.001 TRP C 693 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (25804) covalent geometry : angle 0.52805 / 0.27 (34960) hydrogen bonds : bond 0.05164 / 3.39 ( 1536) hydrogen bonds : angle 3.66281 / 2.62 ( 4536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 294 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6815 (mtp85) cc_final: 0.6279 (mtm-85) REVERT: A 181 THR cc_start: 0.7373 (m) cc_final: 0.7021 (p) REVERT: A 321 LYS cc_start: 0.8024 (tptm) cc_final: 0.7723 (mmmt) REVERT: A 616 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 620 GLU cc_start: 0.8372 (tt0) cc_final: 0.7689 (mt-10) REVERT: A 861 GLN cc_start: 0.7689 (mt0) cc_final: 0.7427 (mt0) REVERT: D 162 ARG cc_start: 0.6821 (mtp85) cc_final: 0.6286 (mtm-85) REVERT: D 181 THR cc_start: 0.7470 (m) cc_final: 0.7102 (p) REVERT: D 620 GLU cc_start: 0.8368 (tt0) cc_final: 0.7691 (mt-10) REVERT: D 861 GLN cc_start: 0.7681 (mt0) cc_final: 0.7471 (mt0) REVERT: B 162 ARG cc_start: 0.6813 (mtp85) cc_final: 0.6210 (mtm-85) REVERT: B 181 THR cc_start: 0.7456 (m) cc_final: 0.7090 (p) REVERT: B 616 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 620 GLU cc_start: 0.8365 (tt0) cc_final: 0.7687 (mt-10) REVERT: B 861 GLN cc_start: 0.7668 (mt0) cc_final: 0.7454 (mt0) REVERT: C 162 ARG cc_start: 0.6809 (mtp85) cc_final: 0.6207 (mtm-85) REVERT: C 181 THR cc_start: 0.7366 (m) cc_final: 0.7008 (p) REVERT: C 616 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 620 GLU cc_start: 0.8360 (tt0) cc_final: 0.7684 (mt-10) REVERT: C 861 GLN cc_start: 0.7672 (mt0) cc_final: 0.7460 (mt0) outliers start: 108 outliers final: 70 residues processed: 374 average time/residue: 0.5050 time to fit residues: 227.8762 Evaluate side-chains 341 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 131 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 140 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.208501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132956 restraints weight = 29295.036| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.34 r_work: 0.3301 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25804 Z= 0.120 Angle : 0.475 8.079 34960 Z= 0.244 Chirality : 0.036 0.131 4060 Planarity : 0.004 0.053 4260 Dihedral : 5.037 42.810 3440 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.25 % Allowed : 25.45 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.16), residues: 2964 helix: 1.54 (0.11), residues: 2212 sheet: -1.67 (0.39), residues: 156 loop : -2.13 (0.21), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.017 0.001 TYR D 191 PHE 0.022 0.001 PHE C 752 TRP 0.015 0.001 TRP C 693 HIS 0.003 0.001 HIS D 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (25804) covalent geometry : angle 0.47480 / 0.24 (34960) hydrogen bonds : bond 0.04336 / 2.83 ( 1536) hydrogen bonds : angle 3.51791 / 2.52 ( 4536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 285 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6845 (mtp85) cc_final: 0.6231 (mtm-85) REVERT: A 321 LYS cc_start: 0.8033 (tptm) cc_final: 0.7762 (mmmt) REVERT: A 353 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6230 (pmm) REVERT: A 445 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 616 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 620 GLU cc_start: 0.8378 (tt0) cc_final: 0.7704 (mt-10) REVERT: A 842 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6129 (tpp-160) REVERT: D 162 ARG cc_start: 0.6847 (mtp85) cc_final: 0.6229 (mtm-85) REVERT: D 353 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6231 (pmm) REVERT: D 620 GLU cc_start: 0.8379 (tt0) cc_final: 0.7707 (mt-10) REVERT: D 631 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: D 842 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6110 (tpp-160) REVERT: D 861 GLN cc_start: 0.7649 (mt0) cc_final: 0.7439 (mt0) REVERT: B 162 ARG cc_start: 0.6838 (mtp85) cc_final: 0.6220 (mtm-85) REVERT: B 353 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6234 (pmm) REVERT: B 616 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 620 GLU cc_start: 0.8373 (tt0) cc_final: 0.7700 (mt-10) REVERT: B 631 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: B 842 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6126 (tpp-160) REVERT: B 861 GLN cc_start: 0.7642 (mt0) cc_final: 0.7427 (mt0) REVERT: C 162 ARG cc_start: 0.6847 (mtp85) cc_final: 0.6223 (mtm-85) REVERT: C 353 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6232 (pmm) REVERT: C 616 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7621 (mt-10) REVERT: C 620 GLU cc_start: 0.8370 (tt0) cc_final: 0.7699 (mt-10) REVERT: C 631 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: C 842 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.6125 (tpp-160) REVERT: C 861 GLN cc_start: 0.7644 (mt0) cc_final: 0.7430 (mt0) outliers start: 113 outliers final: 49 residues processed: 371 average time/residue: 0.4548 time to fit residues: 206.7236 Evaluate side-chains 332 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 842 ARG Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 842 ARG Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 170 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 116 optimal weight: 0.0870 chunk 101 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS B 259 HIS C 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.200754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126009 restraints weight = 29341.842| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.25 r_work: 0.3281 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25804 Z= 0.197 Angle : 0.560 8.722 34960 Z= 0.286 Chirality : 0.040 0.155 4060 Planarity : 0.004 0.056 4260 Dihedral : 5.247 45.116 3438 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.59 % Allowed : 25.71 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.15), residues: 2964 helix: 1.33 (0.11), residues: 2212 sheet: -1.77 (0.38), residues: 156 loop : -2.19 (0.21), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 310 TYR 0.016 0.002 TYR B 191 PHE 0.023 0.002 PHE C 752 TRP 0.014 0.002 TRP A 693 HIS 0.003 0.001 HIS B 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (25804) covalent geometry : angle 0.55976 / 0.29 (34960) hydrogen bonds : bond 0.05486 / 3.60 ( 1536) hydrogen bonds : angle 3.67819 / 2.63 ( 4536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 268 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 162 ARG cc_start: 0.6713 (mtp85) cc_final: 0.6103 (mtm-85) REVERT: A 321 LYS cc_start: 0.7880 (tptm) cc_final: 0.7570 (mmmt) REVERT: A 353 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5999 (pmm) REVERT: A 616 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 620 GLU cc_start: 0.8215 (tt0) cc_final: 0.7462 (mt-10) REVERT: A 861 GLN cc_start: 0.7483 (mt0) cc_final: 0.7208 (mt0) REVERT: D 157 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7534 (mt) REVERT: D 162 ARG cc_start: 0.6717 (mtp85) cc_final: 0.6108 (mtm-85) REVERT: D 353 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6094 (pmm) REVERT: D 620 GLU cc_start: 0.8213 (tt0) cc_final: 0.7466 (mt-10) REVERT: B 157 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7540 (mt) REVERT: B 162 ARG cc_start: 0.6712 (mtp85) cc_final: 0.6100 (mtm-85) REVERT: B 353 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6090 (pmm) REVERT: B 616 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 620 GLU cc_start: 0.8210 (tt0) cc_final: 0.7463 (mt-10) REVERT: C 157 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7518 (mt) REVERT: C 162 ARG cc_start: 0.6712 (mtp85) cc_final: 0.6101 (mtm-85) REVERT: C 353 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.6093 (pmm) REVERT: C 616 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7540 (mt-10) REVERT: C 620 GLU cc_start: 0.8214 (tt0) cc_final: 0.7465 (mt-10) outliers start: 122 outliers final: 73 residues processed: 358 average time/residue: 0.4686 time to fit residues: 205.3734 Evaluate side-chains 348 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 267 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 845 HIS Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 845 HIS Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 845 HIS Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 144 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 204 optimal weight: 0.0980 chunk 161 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 270 optimal weight: 0.0970 chunk 231 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.209690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134405 restraints weight = 29281.518| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.34 r_work: 0.3318 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25804 Z= 0.102 Angle : 0.469 9.623 34960 Z= 0.240 Chirality : 0.036 0.123 4060 Planarity : 0.004 0.052 4260 Dihedral : 4.911 41.250 3438 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.74 % Allowed : 27.41 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.16), residues: 2964 helix: 1.61 (0.11), residues: 2204 sheet: -1.66 (0.38), residues: 156 loop : -1.93 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.015 0.001 TYR B 191 PHE 0.023 0.001 PHE A 752 TRP 0.017 0.001 TRP A 693 HIS 0.005 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (25804) covalent geometry : angle 0.46918 / 0.24 (34960) hydrogen bonds : bond 0.03958 / 2.57 ( 1536) hydrogen bonds : angle 3.44101 / 2.46 ( 4536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 275 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6879 (mtp85) cc_final: 0.6214 (mtm-85) REVERT: A 321 LYS cc_start: 0.7961 (tptm) cc_final: 0.7698 (mmmt) REVERT: A 353 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6217 (pmm) REVERT: A 445 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 620 GLU cc_start: 0.8018 (tt0) cc_final: 0.7516 (mt-10) REVERT: A 631 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: D 162 ARG cc_start: 0.6885 (mtp85) cc_final: 0.6220 (mtm-85) REVERT: D 353 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6371 (pmm) REVERT: D 620 GLU cc_start: 0.8023 (tt0) cc_final: 0.7530 (mt-10) REVERT: D 631 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: B 162 ARG cc_start: 0.6881 (mtp85) cc_final: 0.6214 (mtm-85) REVERT: B 353 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6366 (pmm) REVERT: B 441 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7048 (tp) REVERT: B 620 GLU cc_start: 0.8022 (tt0) cc_final: 0.7506 (mt-10) REVERT: B 631 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: C 162 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6179 (mtm-85) REVERT: C 353 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6295 (pmm) REVERT: C 620 GLU cc_start: 0.8015 (tt0) cc_final: 0.7507 (mt-10) REVERT: C 631 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7434 (tt0) outliers start: 73 outliers final: 44 residues processed: 334 average time/residue: 0.4761 time to fit residues: 194.2088 Evaluate side-chains 310 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 200 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 234 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.207705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131924 restraints weight = 29469.076| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.34 r_work: 0.3291 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25804 Z= 0.142 Angle : 0.510 9.938 34960 Z= 0.261 Chirality : 0.037 0.139 4060 Planarity : 0.004 0.054 4260 Dihedral : 4.893 42.412 3432 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.12 % Allowed : 27.56 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.16), residues: 2964 helix: 1.56 (0.11), residues: 2204 sheet: -1.70 (0.37), residues: 156 loop : -1.96 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.016 0.001 TYR B 191 PHE 0.024 0.001 PHE C 752 TRP 0.019 0.001 TRP D 693 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (25804) covalent geometry : angle 0.51014 / 0.26 (34960) hydrogen bonds : bond 0.04634 / 3.03 ( 1536) hydrogen bonds : angle 3.48747 / 2.50 ( 4536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 269 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6941 (mtp85) cc_final: 0.6305 (mtm-85) REVERT: A 321 LYS cc_start: 0.7993 (tptm) cc_final: 0.7724 (mmmt) REVERT: A 353 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.6044 (pmm) REVERT: A 445 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 616 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 620 GLU cc_start: 0.8366 (tt0) cc_final: 0.7672 (mt-10) REVERT: A 861 GLN cc_start: 0.7669 (mt0) cc_final: 0.7452 (mt0) REVERT: D 162 ARG cc_start: 0.6944 (mtp85) cc_final: 0.6308 (mtm-85) REVERT: D 353 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.6060 (pmm) REVERT: D 616 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 620 GLU cc_start: 0.8370 (tt0) cc_final: 0.7674 (mt-10) REVERT: D 631 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: D 861 GLN cc_start: 0.7672 (mt0) cc_final: 0.7451 (mt0) REVERT: B 162 ARG cc_start: 0.6946 (mtp85) cc_final: 0.6306 (mtm-85) REVERT: B 353 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.6128 (pmm) REVERT: B 616 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7668 (mt-10) REVERT: B 620 GLU cc_start: 0.8367 (tt0) cc_final: 0.7671 (mt-10) REVERT: B 631 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: B 780 CYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7310 (m) REVERT: B 861 GLN cc_start: 0.7663 (mt0) cc_final: 0.7436 (mt0) REVERT: C 162 ARG cc_start: 0.6936 (mtp85) cc_final: 0.6299 (mtm-85) REVERT: C 353 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6080 (pmm) REVERT: C 616 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 620 GLU cc_start: 0.8364 (tt0) cc_final: 0.7668 (mt-10) REVERT: C 631 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: C 861 GLN cc_start: 0.7664 (mt0) cc_final: 0.7440 (mt0) outliers start: 83 outliers final: 57 residues processed: 332 average time/residue: 0.4646 time to fit residues: 188.9439 Evaluate side-chains 334 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 269 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 743 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1009 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 76 optimal weight: 40.0000 chunk 213 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 286 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.209997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134499 restraints weight = 29262.971| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.35 r_work: 0.3319 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25804 Z= 0.104 Angle : 0.470 9.742 34960 Z= 0.240 Chirality : 0.036 0.124 4060 Planarity : 0.004 0.052 4260 Dihedral : 4.740 40.405 3432 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.37 % Allowed : 28.35 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.16), residues: 2964 helix: 1.70 (0.11), residues: 2200 sheet: -1.63 (0.38), residues: 156 loop : -1.93 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 167 TYR 0.015 0.001 TYR C 191 PHE 0.024 0.001 PHE D 752 TRP 0.020 0.001 TRP D 693 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (25804) covalent geometry : angle 0.47024 / 0.24 (34960) hydrogen bonds : bond 0.03902 / 2.54 ( 1536) hydrogen bonds : angle 3.38089 / 2.42 ( 4536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.6840 (mtp85) cc_final: 0.6204 (mtm-85) REVERT: A 321 LYS cc_start: 0.8076 (tptm) cc_final: 0.7826 (mmmt) REVERT: A 353 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.6108 (pmm) REVERT: A 445 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 620 GLU cc_start: 0.8348 (tt0) cc_final: 0.7654 (mt-10) REVERT: A 631 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: D 162 ARG cc_start: 0.6847 (mtp85) cc_final: 0.6196 (mtm-85) REVERT: D 353 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.6100 (pmm) REVERT: D 441 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7117 (tp) REVERT: D 620 GLU cc_start: 0.8345 (tt0) cc_final: 0.7657 (mt-10) REVERT: D 631 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: B 162 ARG cc_start: 0.6849 (mtp85) cc_final: 0.6195 (mtm-85) REVERT: B 353 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.6114 (pmm) REVERT: B 441 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7140 (tp) REVERT: B 620 GLU cc_start: 0.8345 (tt0) cc_final: 0.7647 (mt-10) REVERT: B 631 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: B 780 CYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7278 (m) REVERT: C 162 ARG cc_start: 0.6837 (mtp85) cc_final: 0.6199 (mtm-85) REVERT: C 353 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.6107 (pmm) REVERT: C 441 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7113 (tp) REVERT: C 620 GLU cc_start: 0.8339 (tt0) cc_final: 0.7649 (mt-10) REVERT: C 631 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: C 780 CYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7273 (m) outliers start: 63 outliers final: 42 residues processed: 323 average time/residue: 0.4602 time to fit residues: 181.7301 Evaluate side-chains 326 residues out of total 2804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 867 VAL Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 780 CYS Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 780 CYS Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN B 483 ASN C 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.206944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132259 restraints weight = 29449.428| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.27 r_work: 0.3283 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25804 Z= 0.242 Angle : 0.599 11.178 34960 Z= 0.305 Chirality : 0.042 0.167 4060 Planarity : 0.004 0.057 4260 Dihedral : 5.101 45.179 3432 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.50 % Allowed : 27.18 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.15), residues: 2964 helix: 1.32 (0.11), residues: 2204 sheet: -1.79 (0.36), residues: 156 loop : -1.96 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 288 TYR 0.026 0.002 TYR C 191 PHE 0.024 0.002 PHE C 752 TRP 0.022 0.002 TRP D 693 HIS 0.004 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.24 (25804) covalent geometry : angle 0.59907 / 0.31 (34960) hydrogen bonds : bond 0.05775 / 3.79 ( 1536) hydrogen bonds : angle 3.65821 / 2.62 ( 4536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11249.99 seconds wall clock time: 191 minutes 31.45 seconds (11491.45 seconds total)