Starting phenix.real_space_refine on Sun May 18 20:24:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vi0_43245/05_2025/8vi0_43245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vi0_43245/05_2025/8vi0_43245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vi0_43245/05_2025/8vi0_43245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vi0_43245/05_2025/8vi0_43245.map" model { file = "/net/cci-nas-00/data/ceres_data/8vi0_43245/05_2025/8vi0_43245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vi0_43245/05_2025/8vi0_43245.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 11404 2.51 5 N 2911 2.21 5 O 3049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17454 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5798 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 684} Chain breaks: 2 Chain: "B" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5790 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 683} Chain breaks: 3 Chain: "D" Number of atoms: 5797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5797 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 684} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.00, per 1000 atoms: 0.63 Number of scatterers: 17454 At special positions: 0 Unit cell: (129.6, 135, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3049 8.00 N 2911 7.00 C 11404 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 Links applied BETA1-4 " BGC C 2 " - " BGC C 3 " " BGC E 2 " - " BGC E 3 " " BGC F 2 " - " BGC F 3 " BETA1-5 " BGC C 1 " - " BGC C 2 " " BGC E 1 " - " BGC E 2 " " BGC F 1 " - " BGC F 2 " Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 9 sheets defined 59.2% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 263 through 291 Proline residue: A 269 - end of helix removed outlier: 3.562A pdb=" N HIS A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 319 Processing helix chain 'A' and resid 320 through 323 removed outlier: 4.476A pdb=" N SER A 323 " --> pdb=" O PRO A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.563A pdb=" N LEU A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 376 removed outlier: 3.708A pdb=" N THR A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 394 through 419 removed outlier: 3.600A pdb=" N PHE A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 443 through 469 Processing helix chain 'A' and resid 485 through 489 removed outlier: 4.692A pdb=" N ASN A 489 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 548 Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.724A pdb=" N PHE A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 582 removed outlier: 3.569A pdb=" N LYS A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.564A pdb=" N PHE A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 724 through 732 removed outlier: 3.732A pdb=" N LEU A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 777 through 789 removed outlier: 3.770A pdb=" N LEU A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 831 removed outlier: 3.770A pdb=" N ARG A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 857 Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 879 removed outlier: 3.505A pdb=" N LEU A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 887 through 913 Processing helix chain 'A' and resid 915 through 947 removed outlier: 4.301A pdb=" N HIS A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU A 935 " --> pdb=" O ALA A 931 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 999 Processing helix chain 'A' and resid 1008 through 1023 removed outlier: 3.566A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.888A pdb=" N LEU A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1059 removed outlier: 3.566A pdb=" N LEU A1042 " --> pdb=" O PRO A1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 263 through 291 Proline residue: B 269 - end of helix removed outlier: 3.521A pdb=" N LEU B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 291 " --> pdb=" O TYR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 319 Processing helix chain 'B' and resid 320 through 323 removed outlier: 4.442A pdb=" N SER B 323 " --> pdb=" O PRO B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.538A pdb=" N LEU B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 376 removed outlier: 3.692A pdb=" N THR B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 419 removed outlier: 3.582A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 424 through 430 Processing helix chain 'B' and resid 443 through 469 removed outlier: 3.561A pdb=" N GLU B 447 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 489 removed outlier: 4.695A pdb=" N ASN B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 548 Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.808A pdb=" N PHE B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 582 removed outlier: 3.563A pdb=" N LYS B 582 " --> pdb=" O THR B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 714 through 719 Processing helix chain 'B' and resid 724 through 732 removed outlier: 3.713A pdb=" N LEU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 777 through 789 removed outlier: 3.750A pdb=" N LEU B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 789 " --> pdb=" O LYS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 831 removed outlier: 3.787A pdb=" N ARG B 814 " --> pdb=" O ASN B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 879 removed outlier: 3.648A pdb=" N LEU B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 887 through 913 Processing helix chain 'B' and resid 915 through 947 removed outlier: 4.301A pdb=" N HIS B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 935 " --> pdb=" O ALA B 931 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 999 Processing helix chain 'B' and resid 1008 through 1023 removed outlier: 3.515A pdb=" N ALA B1016 " --> pdb=" O ARG B1012 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B1022 " --> pdb=" O TRP B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1032 removed outlier: 3.785A pdb=" N LEU B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1059 removed outlier: 3.557A pdb=" N LEU B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 269 - end of helix removed outlier: 3.571A pdb=" N HIS D 291 " --> pdb=" O TYR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 319 Processing helix chain 'D' and resid 320 through 323 removed outlier: 4.453A pdb=" N SER D 323 " --> pdb=" O PRO D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.599A pdb=" N LEU D 334 " --> pdb=" O TYR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 376 removed outlier: 3.674A pdb=" N THR D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 394 through 419 removed outlier: 3.634A pdb=" N PHE D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Proline residue: D 413 - end of helix Processing helix chain 'D' and resid 424 through 430 Processing helix chain 'D' and resid 443 through 469 removed outlier: 3.548A pdb=" N GLU D 447 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 removed outlier: 4.681A pdb=" N ASN D 489 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 548 Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.742A pdb=" N PHE D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 removed outlier: 3.547A pdb=" N LYS D 582 " --> pdb=" O THR D 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 579 through 582' Processing helix chain 'D' and resid 606 through 612 removed outlier: 3.525A pdb=" N PHE D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 619 Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 714 through 719 Processing helix chain 'D' and resid 724 through 732 removed outlier: 3.731A pdb=" N LEU D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 777 through 789 removed outlier: 3.746A pdb=" N LEU D 781 " --> pdb=" O THR D 777 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS D 789 " --> pdb=" O LYS D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 831 removed outlier: 3.807A pdb=" N ARG D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 858 Processing helix chain 'D' and resid 861 through 879 removed outlier: 3.526A pdb=" N LEU D 865 " --> pdb=" O THR D 861 " (cutoff:3.500A) Proline residue: D 872 - end of helix Processing helix chain 'D' and resid 887 through 913 Processing helix chain 'D' and resid 915 through 947 removed outlier: 4.378A pdb=" N HIS D 934 " --> pdb=" O GLY D 930 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU D 935 " --> pdb=" O ALA D 931 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE D 936 " --> pdb=" O SER D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 999 Processing helix chain 'D' and resid 1008 through 1023 Processing helix chain 'D' and resid 1023 through 1032 removed outlier: 3.831A pdb=" N LEU D1027 " --> pdb=" O LEU D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1059 removed outlier: 3.643A pdb=" N LEU D1042 " --> pdb=" O PRO D1038 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 499 removed outlier: 7.652A pdb=" N VAL A 384 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL A 518 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS A 386 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 520 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 388 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 350 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR A 387 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 352 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N SER A 389 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 354 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP A 351 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 556 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE A 353 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 585 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 794 " --> pdb=" O CYS A 585 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL A 587 " --> pdb=" O VAL A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 562 removed outlier: 3.935A pdb=" N ARG A 592 " --> pdb=" O PHE A 803 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 261 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 499 removed outlier: 7.660A pdb=" N VAL B 384 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL B 518 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 386 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 520 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL B 388 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 350 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR B 387 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 352 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER B 389 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 354 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP B 351 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 585 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG B 792 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR B 586 " --> pdb=" O ARG B 792 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 561 through 562 removed outlier: 3.902A pdb=" N ARG B 592 " --> pdb=" O PHE B 803 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 257 through 261 Processing sheet with id=AA8, first strand: chain 'D' and resid 496 through 499 removed outlier: 7.630A pdb=" N VAL D 384 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL D 518 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS D 386 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL D 520 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL D 388 " --> pdb=" O VAL D 520 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 350 " --> pdb=" O ALA D 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR D 387 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL D 352 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER D 389 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL D 354 " --> pdb=" O SER D 389 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP D 351 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS D 585 " --> pdb=" O ARG D 633 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 794 " --> pdb=" O CYS D 585 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL D 587 " --> pdb=" O VAL D 794 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 561 through 562 removed outlier: 3.921A pdb=" N ARG D 592 " --> pdb=" O PHE D 803 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2658 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: 5.59 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5419 1.35 - 1.46: 4538 1.46 - 1.58: 7856 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 17948 Sorted by residual: bond pdb=" CG1 ILE A 280 " pdb=" CD1 ILE A 280 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" CB LYS B 740 " pdb=" CG LYS B 740 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CG LEU B 938 " pdb=" CD1 LEU B 938 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CG LYS A 740 " pdb=" CD LYS A 740 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CB LYS A 740 " pdb=" CG LYS A 740 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.54e-01 ... (remaining 17943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 24189 2.33 - 4.66: 171 4.66 - 6.99: 27 6.99 - 9.32: 5 9.32 - 11.65: 3 Bond angle restraints: 24395 Sorted by residual: angle pdb=" CA LEU B 907 " pdb=" CB LEU B 907 " pdb=" CG LEU B 907 " ideal model delta sigma weight residual 116.30 127.95 -11.65 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CA LEU A 907 " pdb=" CB LEU A 907 " pdb=" CG LEU A 907 " ideal model delta sigma weight residual 116.30 127.74 -11.44 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CB LYS A 740 " pdb=" CG LYS A 740 " pdb=" CD LYS A 740 " ideal model delta sigma weight residual 111.30 118.77 -7.47 2.30e+00 1.89e-01 1.06e+01 angle pdb=" CB LYS B 740 " pdb=" CG LYS B 740 " pdb=" CD LYS B 740 " ideal model delta sigma weight residual 111.30 118.74 -7.44 2.30e+00 1.89e-01 1.05e+01 angle pdb=" CA LEU D 907 " pdb=" CB LEU D 907 " pdb=" CG LEU D 907 " ideal model delta sigma weight residual 116.30 127.21 -10.91 3.50e+00 8.16e-02 9.71e+00 ... (remaining 24390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9355 17.96 - 35.92: 957 35.92 - 53.88: 212 53.88 - 71.84: 47 71.84 - 89.80: 6 Dihedral angle restraints: 10577 sinusoidal: 4296 harmonic: 6281 Sorted by residual: dihedral pdb=" CB GLU A 827 " pdb=" CG GLU A 827 " pdb=" CD GLU A 827 " pdb=" OE1 GLU A 827 " ideal model delta sinusoidal sigma weight residual 0.00 89.80 -89.80 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 333 " pdb=" CD ARG A 333 " pdb=" NE ARG A 333 " pdb=" CZ ARG A 333 " ideal model delta sinusoidal sigma weight residual -180.00 -135.20 -44.80 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP B 349 " pdb=" CB ASP B 349 " pdb=" CG ASP B 349 " pdb=" OD1 ASP B 349 " ideal model delta sinusoidal sigma weight residual -30.00 -85.82 55.82 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 10574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2124 0.048 - 0.096: 461 0.096 - 0.144: 94 0.144 - 0.192: 5 0.192 - 0.240: 2 Chirality restraints: 2686 Sorted by residual: chirality pdb=" CB ILE D 280 " pdb=" CA ILE D 280 " pdb=" CG1 ILE D 280 " pdb=" CG2 ILE D 280 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU D 907 " pdb=" CB LEU D 907 " pdb=" CD1 LEU D 907 " pdb=" CD2 LEU D 907 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LEU D 907 " pdb=" N LEU D 907 " pdb=" C LEU D 907 " pdb=" CB LEU D 907 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 2683 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 978 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 979 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 979 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 979 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 257 " -0.009 2.00e-02 2.50e+03 8.71e-03 1.90e+00 pdb=" CG TRP A 257 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 257 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 257 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 257 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 257 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 978 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO D 979 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 979 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 979 " -0.019 5.00e-02 4.00e+02 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 375 2.71 - 3.26: 17087 3.26 - 3.81: 28556 3.81 - 4.35: 35239 4.35 - 4.90: 59822 Nonbonded interactions: 141079 Sorted by model distance: nonbonded pdb=" OD1 ASN D 606 " pdb=" O6 BGC F 2 " model vdw 2.166 3.040 nonbonded pdb=" OE2 GLU B 456 " pdb=" OH TYR D 435 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLU B 426 " pdb=" OH TYR B 455 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU A 456 " pdb=" OH TYR B 435 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 435 " pdb=" OE2 GLU D 456 " model vdw 2.230 3.040 ... (remaining 141074 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 249 through 853 or resid 855 through 864 or (resid 865 and \ (name N or name CA or name C or name O or name CB or name CG or name CD2)) or r \ esid 866 through 1059)) selection = (chain 'B' and (resid 249 through 864 or (resid 865 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD2)) or resid 866 through 1059)) selection = (chain 'D' and (resid 249 through 853 or resid 855 through 1059)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } 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: 3.110 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: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 40.930 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.002 0.048 17954 Z= 0.102 Angle : 0.500 11.646 24413 Z= 0.258 Chirality : 0.040 0.240 2686 Planarity : 0.004 0.035 3042 Dihedral : 15.046 89.805 6547 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.45 % Allowed : 13.82 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2151 helix: 2.11 (0.16), residues: 1166 sheet: 1.58 (0.47), residues: 132 loop : -0.53 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 257 HIS 0.004 0.001 HIS B 917 PHE 0.009 0.001 PHE D 925 TYR 0.014 0.001 TYR D 270 ARG 0.009 0.000 ARG D 820 Details of bonding type rmsd link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 0.88019 ( 9) hydrogen bonds : bond 0.11516 ( 898) hydrogen bonds : angle 5.13382 ( 2658) glycosidic custom : bond 0.00191 ( 3) glycosidic custom : angle 0.75257 ( 9) covalent geometry : bond 0.00221 (17948) covalent geometry : angle 0.49922 (24395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.7564 (t80) cc_final: 0.7263 (t80) REVERT: A 840 TYR cc_start: 0.6787 (m-80) cc_final: 0.6498 (m-80) REVERT: A 922 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8055 (t0) REVERT: B 277 ARG cc_start: 0.7961 (ttt180) cc_final: 0.7531 (ttt-90) REVERT: B 506 VAL cc_start: 0.6366 (OUTLIER) cc_final: 0.6164 (p) REVERT: B 617 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 820 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.7926 (ttp80) REVERT: B 922 ASN cc_start: 0.8733 (t0) cc_final: 0.8353 (t0) REVERT: B 1018 TRP cc_start: 0.7806 (t60) cc_final: 0.7562 (t60) REVERT: D 275 VAL cc_start: 0.8183 (t) cc_final: 0.7851 (t) REVERT: D 491 ARG cc_start: 0.8528 (mtt90) cc_final: 0.8302 (ptp90) REVERT: D 528 TYR cc_start: 0.7716 (m-80) cc_final: 0.7401 (m-80) REVERT: D 895 MET cc_start: 0.6647 (mmp) cc_final: 0.6434 (mmp) outliers start: 27 outliers final: 15 residues processed: 294 average time/residue: 0.9848 time to fit residues: 332.9622 Evaluate side-chains 278 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 851 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 196 optimal weight: 0.0870 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 714 GLN B 817 GLN B 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114523 restraints weight = 20821.291| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.32 r_work: 0.3192 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17954 Z= 0.127 Angle : 0.499 9.264 24413 Z= 0.254 Chirality : 0.042 0.177 2686 Planarity : 0.004 0.036 3042 Dihedral : 4.671 58.292 2506 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.36 % Allowed : 15.96 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2151 helix: 2.19 (0.16), residues: 1174 sheet: 1.73 (0.47), residues: 130 loop : -0.66 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 257 HIS 0.003 0.001 HIS A 789 PHE 0.011 0.001 PHE B 637 TYR 0.016 0.001 TYR D 858 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd link_BETA1-4 : bond 0.00384 ( 3) link_BETA1-4 : angle 1.16883 ( 9) hydrogen bonds : bond 0.03880 ( 898) hydrogen bonds : angle 4.05923 ( 2658) glycosidic custom : bond 0.00133 ( 3) glycosidic custom : angle 0.86407 ( 9) covalent geometry : bond 0.00297 (17948) covalent geometry : angle 0.49813 (24395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 TRP cc_start: 0.7165 (p-90) cc_final: 0.6902 (p-90) REVERT: A 273 ILE cc_start: 0.8033 (tp) cc_final: 0.7775 (pp) REVERT: A 307 GLU cc_start: 0.6383 (mp0) cc_final: 0.6082 (mp0) REVERT: A 409 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8314 (mtt90) REVERT: A 426 GLU cc_start: 0.8561 (tp30) cc_final: 0.7739 (tp30) REVERT: A 840 TYR cc_start: 0.6723 (m-80) cc_final: 0.6223 (m-80) REVERT: B 506 VAL cc_start: 0.6600 (OUTLIER) cc_final: 0.6392 (p) REVERT: B 820 ARG cc_start: 0.7830 (ttp-110) cc_final: 0.7381 (ttp80) REVERT: B 880 LYS cc_start: 0.7090 (mmtm) cc_final: 0.6820 (mmmt) REVERT: B 936 PHE cc_start: 0.7440 (m-80) cc_final: 0.7147 (m-80) REVERT: D 426 GLU cc_start: 0.8496 (tp30) cc_final: 0.8248 (tp30) REVERT: D 491 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7185 (ptp90) REVERT: D 840 TYR cc_start: 0.6665 (m-80) cc_final: 0.6233 (m-80) REVERT: D 921 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7880 (mmm-85) REVERT: D 938 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6753 (mp) outliers start: 44 outliers final: 13 residues processed: 300 average time/residue: 0.9850 time to fit residues: 339.4158 Evaluate side-chains 270 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 36 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN B 268 ASN B 917 HIS B 924 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108409 restraints weight = 20638.069| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.25 r_work: 0.3147 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17954 Z= 0.145 Angle : 0.513 12.324 24413 Z= 0.258 Chirality : 0.042 0.152 2686 Planarity : 0.004 0.036 3042 Dihedral : 4.106 52.279 2487 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.32 % Allowed : 16.71 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2151 helix: 2.16 (0.15), residues: 1168 sheet: 1.55 (0.48), residues: 131 loop : -0.74 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 257 HIS 0.004 0.001 HIS B 789 PHE 0.010 0.001 PHE D 925 TYR 0.016 0.001 TYR D 858 ARG 0.006 0.000 ARG D 820 Details of bonding type rmsd link_BETA1-4 : bond 0.00343 ( 3) link_BETA1-4 : angle 1.01142 ( 9) hydrogen bonds : bond 0.04085 ( 898) hydrogen bonds : angle 3.98706 ( 2658) glycosidic custom : bond 0.00148 ( 3) glycosidic custom : angle 0.77945 ( 9) covalent geometry : bond 0.00352 (17948) covalent geometry : angle 0.51267 (24395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 GLU cc_start: 0.8639 (tp30) cc_final: 0.7801 (tp30) REVERT: B 259 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7649 (mppt) REVERT: B 307 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: B 317 ASP cc_start: 0.8087 (t0) cc_final: 0.7023 (m-30) REVERT: B 335 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8406 (p) REVERT: B 491 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7608 (ptp-110) REVERT: B 506 VAL cc_start: 0.7194 (OUTLIER) cc_final: 0.6986 (p) REVERT: B 528 TYR cc_start: 0.7685 (m-80) cc_final: 0.7048 (m-80) REVERT: B 614 MET cc_start: 0.8395 (mmm) cc_final: 0.8184 (mmm) REVERT: B 820 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7443 (ttp80) REVERT: B 880 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6957 (mmmt) REVERT: B 921 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7213 (ttm110) REVERT: B 1020 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7218 (tp) REVERT: D 360 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7153 (mpm) REVERT: D 426 GLU cc_start: 0.8586 (tp30) cc_final: 0.8376 (tp30) REVERT: D 528 TYR cc_start: 0.7962 (m-80) cc_final: 0.7627 (m-80) REVERT: D 749 LYS cc_start: 0.7546 (tptp) cc_final: 0.6958 (mtpp) REVERT: D 792 ARG cc_start: 0.7537 (mpt180) cc_final: 0.7111 (mpp-170) REVERT: D 808 PRO cc_start: 0.7773 (Cg_exo) cc_final: 0.7557 (Cg_endo) REVERT: D 860 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6390 (tp) REVERT: D 906 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6538 (mp) REVERT: D 936 PHE cc_start: 0.7857 (m-80) cc_final: 0.7584 (m-80) REVERT: D 938 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6997 (mp) outliers start: 62 outliers final: 29 residues processed: 315 average time/residue: 0.9832 time to fit residues: 356.5547 Evaluate side-chains 296 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1020 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 120 optimal weight: 0.4980 chunk 126 optimal weight: 0.0670 chunk 1 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 203 optimal weight: 0.1980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS B 268 ASN D 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113798 restraints weight = 20750.907| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.24 r_work: 0.3168 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17954 Z= 0.109 Angle : 0.476 8.534 24413 Z= 0.241 Chirality : 0.041 0.174 2686 Planarity : 0.004 0.044 3042 Dihedral : 3.980 53.937 2486 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.27 % Allowed : 17.84 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 2151 helix: 2.21 (0.15), residues: 1179 sheet: 1.66 (0.48), residues: 131 loop : -0.69 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 911 HIS 0.005 0.001 HIS D 291 PHE 0.014 0.001 PHE B 637 TYR 0.015 0.001 TYR D 858 ARG 0.006 0.000 ARG A 820 Details of bonding type rmsd link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 1.01348 ( 9) hydrogen bonds : bond 0.03638 ( 898) hydrogen bonds : angle 3.87482 ( 2658) glycosidic custom : bond 0.00189 ( 3) glycosidic custom : angle 0.72789 ( 9) covalent geometry : bond 0.00252 (17948) covalent geometry : angle 0.47605 (24395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7941 (t0) cc_final: 0.7030 (m-30) REVERT: B 259 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7657 (mppt) REVERT: B 317 ASP cc_start: 0.8056 (t0) cc_final: 0.6984 (m-30) REVERT: B 335 SER cc_start: 0.8595 (t) cc_final: 0.8382 (p) REVERT: B 360 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7888 (mpp) REVERT: B 426 GLU cc_start: 0.8610 (tp30) cc_final: 0.8055 (tp30) REVERT: B 506 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6969 (p) REVERT: B 528 TYR cc_start: 0.7669 (m-80) cc_final: 0.7068 (m-80) REVERT: B 637 PHE cc_start: 0.8311 (m-10) cc_final: 0.8110 (m-10) REVERT: B 820 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.7441 (ttp80) REVERT: B 921 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7245 (ttm110) REVERT: D 307 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: D 360 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7129 (mpm) REVERT: D 426 GLU cc_start: 0.8590 (tp30) cc_final: 0.8377 (tp30) REVERT: D 445 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8216 (mm) REVERT: D 528 TYR cc_start: 0.7951 (m-80) cc_final: 0.7635 (m-80) REVERT: D 740 LYS cc_start: 0.8054 (mppt) cc_final: 0.7758 (mmmt) REVERT: D 749 LYS cc_start: 0.7695 (tptp) cc_final: 0.7102 (mtpp) REVERT: D 792 ARG cc_start: 0.7505 (mpt180) cc_final: 0.7074 (mpp-170) REVERT: D 808 PRO cc_start: 0.7775 (Cg_exo) cc_final: 0.7555 (Cg_endo) REVERT: D 840 TYR cc_start: 0.6759 (m-80) cc_final: 0.6485 (m-80) REVERT: D 860 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6353 (tp) REVERT: D 906 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6454 (mp) REVERT: D 938 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6942 (mp) outliers start: 61 outliers final: 27 residues processed: 301 average time/residue: 1.0179 time to fit residues: 352.1182 Evaluate side-chains 291 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1022 HIS Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 921 ARG Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 185 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 714 GLN A 816 HIS A 922 ASN B 606 ASN B 816 HIS B 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 503 GLN D1022 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105254 restraints weight = 21163.702| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.28 r_work: 0.3059 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 17954 Z= 0.272 Angle : 0.599 8.536 24413 Z= 0.306 Chirality : 0.046 0.167 2686 Planarity : 0.005 0.052 3042 Dihedral : 4.382 56.448 2486 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.93 % Allowed : 16.60 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2151 helix: 1.93 (0.15), residues: 1153 sheet: 1.49 (0.50), residues: 131 loop : -0.97 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 919 HIS 0.007 0.001 HIS D 291 PHE 0.019 0.002 PHE B 637 TYR 0.016 0.002 TYR D 858 ARG 0.007 0.001 ARG D 820 Details of bonding type rmsd link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 1.14038 ( 9) hydrogen bonds : bond 0.05212 ( 898) hydrogen bonds : angle 4.14120 ( 2658) glycosidic custom : bond 0.00096 ( 3) glycosidic custom : angle 1.06050 ( 9) covalent geometry : bond 0.00687 (17948) covalent geometry : angle 0.59820 (24395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 287 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.8004 (t0) cc_final: 0.7046 (m-30) REVERT: A 427 TRP cc_start: 0.9196 (m-90) cc_final: 0.8983 (m-90) REVERT: A 433 VAL cc_start: 0.7722 (t) cc_final: 0.7456 (m) REVERT: A 572 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8498 (mpp) REVERT: A 749 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7489 (tptp) REVERT: A 808 PRO cc_start: 0.7901 (Cg_exo) cc_final: 0.7605 (Cg_endo) REVERT: A 869 CYS cc_start: 0.8128 (m) cc_final: 0.7597 (m) REVERT: A 933 SER cc_start: 0.8639 (m) cc_final: 0.8178 (p) REVERT: A 936 PHE cc_start: 0.7721 (m-80) cc_final: 0.7281 (m-80) REVERT: A 940 GLN cc_start: 0.7307 (mt0) cc_final: 0.7069 (mp10) REVERT: A 1012 ARG cc_start: 0.4168 (OUTLIER) cc_final: 0.3857 (ttt180) REVERT: B 259 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7688 (mppt) REVERT: B 307 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: B 317 ASP cc_start: 0.8081 (t0) cc_final: 0.7014 (m-30) REVERT: B 360 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8034 (mpp) REVERT: B 426 GLU cc_start: 0.8716 (tp30) cc_final: 0.8074 (tp30) REVERT: B 433 VAL cc_start: 0.7804 (t) cc_final: 0.7564 (m) REVERT: B 792 ARG cc_start: 0.7681 (mpt180) cc_final: 0.7271 (mpp-170) REVERT: B 880 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7768 (mppt) REVERT: B 921 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7458 (ttm110) REVERT: B 935 LEU cc_start: 0.7853 (mt) cc_final: 0.7471 (tt) REVERT: D 339 GLU cc_start: 0.7755 (tt0) cc_final: 0.7371 (tp30) REVERT: D 349 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: D 433 VAL cc_start: 0.7696 (t) cc_final: 0.7412 (m) REVERT: D 528 TYR cc_start: 0.7997 (m-80) cc_final: 0.7773 (m-80) REVERT: D 624 ILE cc_start: 0.8803 (mt) cc_final: 0.8504 (mp) REVERT: D 792 ARG cc_start: 0.7601 (mpt180) cc_final: 0.7197 (mpp-170) REVERT: D 808 PRO cc_start: 0.7951 (Cg_exo) cc_final: 0.7733 (Cg_endo) REVERT: D 816 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7557 (m90) REVERT: D 860 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6381 (mt) REVERT: D 906 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6694 (mp) REVERT: D 938 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6997 (mp) outliers start: 92 outliers final: 45 residues processed: 340 average time/residue: 0.9771 time to fit residues: 381.9826 Evaluate side-chains 323 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 268 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1012 ARG Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 921 ARG Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 816 HIS Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 156 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 922 ASN B 606 ASN B 817 GLN B 922 ASN B 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108301 restraints weight = 20954.524| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.25 r_work: 0.3097 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17954 Z= 0.148 Angle : 0.545 13.682 24413 Z= 0.274 Chirality : 0.042 0.154 2686 Planarity : 0.004 0.049 3042 Dihedral : 4.091 44.343 2484 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.91 % Allowed : 18.48 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2151 helix: 2.03 (0.15), residues: 1153 sheet: 1.60 (0.50), residues: 131 loop : -0.98 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 911 HIS 0.004 0.001 HIS A 917 PHE 0.011 0.001 PHE D 925 TYR 0.016 0.001 TYR B 552 ARG 0.009 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00364 ( 3) link_BETA1-4 : angle 1.12542 ( 9) hydrogen bonds : bond 0.04345 ( 898) hydrogen bonds : angle 4.03099 ( 2658) glycosidic custom : bond 0.00125 ( 3) glycosidic custom : angle 0.76929 ( 9) covalent geometry : bond 0.00359 (17948) covalent geometry : angle 0.54436 (24395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 271 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7942 (t0) cc_final: 0.7033 (m-30) REVERT: A 427 TRP cc_start: 0.9174 (m-90) cc_final: 0.8964 (m-90) REVERT: A 433 VAL cc_start: 0.7704 (t) cc_final: 0.7453 (m) REVERT: A 808 PRO cc_start: 0.7888 (Cg_exo) cc_final: 0.7587 (Cg_endo) REVERT: A 933 SER cc_start: 0.8605 (m) cc_final: 0.8171 (p) REVERT: A 936 PHE cc_start: 0.7844 (m-80) cc_final: 0.7327 (m-80) REVERT: B 256 LEU cc_start: 0.7145 (mt) cc_final: 0.6836 (mp) REVERT: B 259 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7646 (mppt) REVERT: B 307 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: B 317 ASP cc_start: 0.8121 (t0) cc_final: 0.7100 (m-30) REVERT: B 360 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7965 (mpp) REVERT: B 426 GLU cc_start: 0.8666 (tp30) cc_final: 0.8067 (tp30) REVERT: B 433 VAL cc_start: 0.7843 (t) cc_final: 0.7609 (m) REVERT: B 808 PRO cc_start: 0.8079 (Cg_exo) cc_final: 0.7830 (Cg_endo) REVERT: B 907 LEU cc_start: 0.7512 (mt) cc_final: 0.7301 (mp) REVERT: B 935 LEU cc_start: 0.7807 (mt) cc_final: 0.7429 (tt) REVERT: D 307 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: D 360 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7241 (mpm) REVERT: D 433 VAL cc_start: 0.7643 (t) cc_final: 0.7382 (m) REVERT: D 624 ILE cc_start: 0.8782 (mt) cc_final: 0.8520 (mp) REVERT: D 740 LYS cc_start: 0.8024 (mppt) cc_final: 0.7807 (mmmt) REVERT: D 792 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7145 (mpp-170) REVERT: D 860 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6301 (mt) REVERT: D 906 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6658 (mp) REVERT: D 938 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6992 (mp) outliers start: 73 outliers final: 38 residues processed: 313 average time/residue: 0.9789 time to fit residues: 352.4946 Evaluate side-chains 305 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 39 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.0050 chunk 89 optimal weight: 0.9980 overall best weight: 1.0156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 940 GLN B1022 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106629 restraints weight = 20933.784| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.30 r_work: 0.3080 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17954 Z= 0.182 Angle : 0.556 11.463 24413 Z= 0.281 Chirality : 0.043 0.156 2686 Planarity : 0.004 0.056 3042 Dihedral : 4.139 42.424 2483 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.07 % Allowed : 18.85 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2151 helix: 1.96 (0.15), residues: 1154 sheet: 1.54 (0.50), residues: 131 loop : -1.03 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 919 HIS 0.005 0.001 HIS A 917 PHE 0.013 0.001 PHE D 284 TYR 0.015 0.001 TYR D 858 ARG 0.019 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00328 ( 3) link_BETA1-4 : angle 1.11014 ( 9) hydrogen bonds : bond 0.04480 ( 898) hydrogen bonds : angle 4.03940 ( 2658) glycosidic custom : bond 0.00141 ( 3) glycosidic custom : angle 0.87908 ( 9) covalent geometry : bond 0.00452 (17948) covalent geometry : angle 0.55594 (24395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 270 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7884 (t0) cc_final: 0.6982 (m-30) REVERT: A 427 TRP cc_start: 0.9176 (m-90) cc_final: 0.8949 (m-90) REVERT: A 433 VAL cc_start: 0.7679 (t) cc_final: 0.7419 (m) REVERT: A 596 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4988 (pp) REVERT: A 749 LYS cc_start: 0.8040 (ptmt) cc_final: 0.7367 (tptp) REVERT: A 808 PRO cc_start: 0.7997 (Cg_exo) cc_final: 0.7715 (Cg_endo) REVERT: A 933 SER cc_start: 0.8521 (m) cc_final: 0.8081 (p) REVERT: A 936 PHE cc_start: 0.7704 (m-80) cc_final: 0.7469 (m-80) REVERT: B 256 LEU cc_start: 0.6949 (mt) cc_final: 0.6639 (mp) REVERT: B 259 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7620 (mppt) REVERT: B 307 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5955 (mp0) REVERT: B 317 ASP cc_start: 0.8037 (t0) cc_final: 0.6978 (m-30) REVERT: B 360 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7907 (mpp) REVERT: B 426 GLU cc_start: 0.8634 (tp30) cc_final: 0.7951 (tp30) REVERT: B 433 VAL cc_start: 0.7816 (t) cc_final: 0.7571 (m) REVERT: B 596 ILE cc_start: 0.5642 (OUTLIER) cc_final: 0.5235 (pp) REVERT: B 637 PHE cc_start: 0.8547 (m-10) cc_final: 0.8298 (m-10) REVERT: B 880 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7318 (mppt) REVERT: B 935 LEU cc_start: 0.7715 (mt) cc_final: 0.7363 (tt) REVERT: D 259 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7622 (mppt) REVERT: D 272 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7230 (mm) REVERT: D 307 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: D 349 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: D 433 VAL cc_start: 0.7623 (t) cc_final: 0.7351 (m) REVERT: D 611 ASP cc_start: 0.8015 (m-30) cc_final: 0.7045 (t0) REVERT: D 624 ILE cc_start: 0.8740 (mt) cc_final: 0.8463 (mp) REVERT: D 792 ARG cc_start: 0.7555 (mpt180) cc_final: 0.7145 (mpp-170) REVERT: D 860 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6257 (mt) REVERT: D 938 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6933 (mp) outliers start: 76 outliers final: 42 residues processed: 319 average time/residue: 1.0030 time to fit residues: 368.5673 Evaluate side-chains 311 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 0.0000 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 604 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 = 0.3936 r_free = 0.3936 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109742 restraints weight = 20839.934| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.25 r_work: 0.3132 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17954 Z= 0.127 Angle : 0.536 14.137 24413 Z= 0.266 Chirality : 0.041 0.153 2686 Planarity : 0.004 0.066 3042 Dihedral : 4.008 39.548 2483 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.48 % Allowed : 19.71 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2151 helix: 2.06 (0.15), residues: 1160 sheet: 1.65 (0.49), residues: 131 loop : -0.98 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 911 HIS 0.005 0.001 HIS A 917 PHE 0.013 0.001 PHE D 284 TYR 0.020 0.001 TYR A 287 ARG 0.017 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00452 ( 3) link_BETA1-4 : angle 1.06385 ( 9) hydrogen bonds : bond 0.03969 ( 898) hydrogen bonds : angle 3.95388 ( 2658) glycosidic custom : bond 0.00207 ( 3) glycosidic custom : angle 0.76661 ( 9) covalent geometry : bond 0.00301 (17948) covalent geometry : angle 0.53558 (24395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 269 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.8017 (t0) cc_final: 0.7144 (m-30) REVERT: A 433 VAL cc_start: 0.7708 (t) cc_final: 0.7477 (m) REVERT: A 596 ILE cc_start: 0.5365 (OUTLIER) cc_final: 0.4970 (pp) REVERT: A 808 PRO cc_start: 0.8117 (Cg_exo) cc_final: 0.7900 (Cg_endo) REVERT: A 933 SER cc_start: 0.8566 (m) cc_final: 0.8132 (p) REVERT: A 936 PHE cc_start: 0.7792 (m-80) cc_final: 0.7457 (m-80) REVERT: A 940 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: A 1012 ARG cc_start: 0.4157 (OUTLIER) cc_final: 0.3955 (ttt180) REVERT: B 256 LEU cc_start: 0.7052 (mt) cc_final: 0.6741 (mp) REVERT: B 259 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7675 (mppt) REVERT: B 307 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: B 317 ASP cc_start: 0.8005 (t0) cc_final: 0.6922 (m-30) REVERT: B 360 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7962 (mpp) REVERT: B 426 GLU cc_start: 0.8624 (tp30) cc_final: 0.7973 (tp30) REVERT: B 427 TRP cc_start: 0.9100 (m-90) cc_final: 0.8855 (m-90) REVERT: B 433 VAL cc_start: 0.7876 (t) cc_final: 0.7675 (m) REVERT: B 596 ILE cc_start: 0.5629 (OUTLIER) cc_final: 0.5197 (pp) REVERT: B 637 PHE cc_start: 0.8489 (m-10) cc_final: 0.8225 (m-10) REVERT: B 880 LYS cc_start: 0.7814 (mmmm) cc_final: 0.7317 (mppt) REVERT: B 924 GLN cc_start: 0.6441 (mt0) cc_final: 0.5965 (tt0) REVERT: B 935 LEU cc_start: 0.7819 (mt) cc_final: 0.7488 (tt) REVERT: D 257 TRP cc_start: 0.7065 (p-90) cc_final: 0.6710 (p-90) REVERT: D 259 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7629 (mppt) REVERT: D 307 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: D 349 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: D 360 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7225 (mpm) REVERT: D 433 VAL cc_start: 0.7653 (t) cc_final: 0.7408 (m) REVERT: D 437 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8125 (tttp) REVERT: D 611 ASP cc_start: 0.7988 (m-30) cc_final: 0.6978 (t0) REVERT: D 624 ILE cc_start: 0.8772 (mt) cc_final: 0.8516 (mp) REVERT: D 740 LYS cc_start: 0.7990 (mppt) cc_final: 0.7763 (mmmt) REVERT: D 792 ARG cc_start: 0.7680 (mpt180) cc_final: 0.7291 (mpp-170) REVERT: D 860 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6253 (mt) REVERT: D 938 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6956 (mp) outliers start: 65 outliers final: 40 residues processed: 310 average time/residue: 0.9288 time to fit residues: 334.0679 Evaluate side-chains 308 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1012 ARG Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 113 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 155 optimal weight: 0.0060 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS B 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107966 restraints weight = 20910.695| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.32 r_work: 0.3101 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17954 Z= 0.148 Angle : 0.553 12.271 24413 Z= 0.274 Chirality : 0.042 0.215 2686 Planarity : 0.004 0.069 3042 Dihedral : 4.002 38.227 2483 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.70 % Allowed : 19.60 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.18), residues: 2151 helix: 2.04 (0.15), residues: 1160 sheet: 1.64 (0.49), residues: 131 loop : -0.98 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 919 HIS 0.005 0.001 HIS A 917 PHE 0.013 0.001 PHE D 284 TYR 0.020 0.001 TYR A 287 ARG 0.018 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 1.10600 ( 9) hydrogen bonds : bond 0.04134 ( 898) hydrogen bonds : angle 3.95179 ( 2658) glycosidic custom : bond 0.00157 ( 3) glycosidic custom : angle 0.81508 ( 9) covalent geometry : bond 0.00362 (17948) covalent geometry : angle 0.55273 (24395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7925 (t0) cc_final: 0.7034 (m-30) REVERT: A 433 VAL cc_start: 0.7689 (t) cc_final: 0.7454 (m) REVERT: A 596 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.5005 (pp) REVERT: A 749 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7413 (tptp) REVERT: A 933 SER cc_start: 0.8457 (m) cc_final: 0.8061 (p) REVERT: A 936 PHE cc_start: 0.7656 (m-80) cc_final: 0.7313 (m-80) REVERT: A 940 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: B 256 LEU cc_start: 0.6944 (mt) cc_final: 0.6633 (mp) REVERT: B 307 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5985 (mp0) REVERT: B 317 ASP cc_start: 0.8027 (t0) cc_final: 0.6980 (m-30) REVERT: B 360 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7886 (mpp) REVERT: B 426 GLU cc_start: 0.8592 (tp30) cc_final: 0.7870 (tp30) REVERT: B 427 TRP cc_start: 0.9067 (m-90) cc_final: 0.8786 (m-90) REVERT: B 433 VAL cc_start: 0.7852 (t) cc_final: 0.7649 (m) REVERT: B 596 ILE cc_start: 0.5577 (OUTLIER) cc_final: 0.5172 (pp) REVERT: B 740 LYS cc_start: 0.7880 (mppt) cc_final: 0.7676 (mmmt) REVERT: B 880 LYS cc_start: 0.7810 (mmmm) cc_final: 0.7520 (mmmt) REVERT: B 924 GLN cc_start: 0.6389 (mt0) cc_final: 0.6035 (tt0) REVERT: B 935 LEU cc_start: 0.7703 (mt) cc_final: 0.7387 (tt) REVERT: D 257 TRP cc_start: 0.7059 (p-90) cc_final: 0.6680 (p-90) REVERT: D 259 LYS cc_start: 0.7813 (mtmt) cc_final: 0.7574 (mppt) REVERT: D 307 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6214 (mp0) REVERT: D 349 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: D 433 VAL cc_start: 0.7559 (t) cc_final: 0.7318 (m) REVERT: D 596 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.4849 (pp) REVERT: D 624 ILE cc_start: 0.8719 (mt) cc_final: 0.8432 (mp) REVERT: D 740 LYS cc_start: 0.8123 (mppt) cc_final: 0.7860 (mmmt) REVERT: D 792 ARG cc_start: 0.7541 (mpt180) cc_final: 0.7135 (mpp-170) REVERT: D 860 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6200 (mt) REVERT: D 938 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6934 (mp) outliers start: 69 outliers final: 41 residues processed: 312 average time/residue: 0.9450 time to fit residues: 342.7400 Evaluate side-chains 310 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 809 ILE Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 159 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 178 optimal weight: 0.5980 chunk 101 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS B 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108703 restraints weight = 20889.722| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.33 r_work: 0.3126 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.003 0.054 17954 Z= 0.131 Angle : 0.559 14.577 24413 Z= 0.275 Chirality : 0.042 0.163 2686 Planarity : 0.004 0.075 3042 Dihedral : 3.981 38.396 2483 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.37 % Allowed : 19.93 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2151 helix: 2.08 (0.15), residues: 1154 sheet: 1.67 (0.49), residues: 131 loop : -0.96 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 911 HIS 0.006 0.001 HIS A 286 PHE 0.013 0.001 PHE D 284 TYR 0.015 0.001 TYR D 858 ARG 0.018 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00399 ( 3) link_BETA1-4 : angle 1.10022 ( 9) hydrogen bonds : bond 0.04001 ( 898) hydrogen bonds : angle 3.92369 ( 2658) glycosidic custom : bond 0.00171 ( 3) glycosidic custom : angle 0.76652 ( 9) covalent geometry : bond 0.00316 (17948) covalent geometry : angle 0.55833 (24395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7965 (t0) cc_final: 0.7011 (m-30) REVERT: A 433 VAL cc_start: 0.7734 (t) cc_final: 0.7517 (m) REVERT: A 572 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: A 596 ILE cc_start: 0.5410 (OUTLIER) cc_final: 0.5039 (pp) REVERT: A 749 LYS cc_start: 0.8013 (ptmt) cc_final: 0.7445 (tptp) REVERT: A 933 SER cc_start: 0.8532 (m) cc_final: 0.8107 (p) REVERT: A 936 PHE cc_start: 0.7874 (m-80) cc_final: 0.7526 (m-80) REVERT: A 940 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: B 256 LEU cc_start: 0.7005 (mt) cc_final: 0.6707 (mp) REVERT: B 307 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: B 317 ASP cc_start: 0.7879 (t0) cc_final: 0.6728 (m-30) REVERT: B 360 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7850 (mpp) REVERT: B 426 GLU cc_start: 0.8591 (tp30) cc_final: 0.7887 (tp30) REVERT: B 427 TRP cc_start: 0.9019 (m-90) cc_final: 0.8751 (m-90) REVERT: B 596 ILE cc_start: 0.5607 (OUTLIER) cc_final: 0.5199 (pp) REVERT: B 637 PHE cc_start: 0.8501 (m-10) cc_final: 0.8226 (m-10) REVERT: B 880 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7544 (mmmt) REVERT: B 924 GLN cc_start: 0.6440 (mt0) cc_final: 0.6152 (tt0) REVERT: B 935 LEU cc_start: 0.7794 (mt) cc_final: 0.7456 (tt) REVERT: D 257 TRP cc_start: 0.7001 (p-90) cc_final: 0.6721 (p-90) REVERT: D 259 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7620 (mppt) REVERT: D 307 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: D 349 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: D 360 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7185 (mpm) REVERT: D 433 VAL cc_start: 0.7608 (t) cc_final: 0.7355 (m) REVERT: D 437 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8137 (tttm) REVERT: D 596 ILE cc_start: 0.5369 (OUTLIER) cc_final: 0.4888 (pp) REVERT: D 611 ASP cc_start: 0.8019 (m-30) cc_final: 0.6876 (t0) REVERT: D 624 ILE cc_start: 0.8751 (mt) cc_final: 0.8502 (mp) REVERT: D 740 LYS cc_start: 0.8238 (mppt) cc_final: 0.7987 (mmmt) REVERT: D 792 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7144 (mpp-170) REVERT: D 860 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6228 (mt) REVERT: D 938 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7000 (mp) outliers start: 63 outliers final: 44 residues processed: 310 average time/residue: 0.9529 time to fit residues: 341.5271 Evaluate side-chains 312 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 809 ILE Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 170 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 192 optimal weight: 0.3980 chunk 210 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS B 268 ASN B 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.166031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109578 restraints weight = 20832.384| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.27 r_work: 0.3129 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17954 Z= 0.134 Angle : 0.557 13.734 24413 Z= 0.274 Chirality : 0.042 0.157 2686 Planarity : 0.004 0.074 3042 Dihedral : 3.949 38.501 2483 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.54 % Allowed : 20.03 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2151 helix: 2.09 (0.15), residues: 1156 sheet: 1.65 (0.49), residues: 131 loop : -0.95 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 911 HIS 0.006 0.001 HIS A 286 PHE 0.013 0.001 PHE D 284 TYR 0.015 0.001 TYR D 858 ARG 0.018 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00347 ( 3) link_BETA1-4 : angle 1.11291 ( 9) hydrogen bonds : bond 0.03965 ( 898) hydrogen bonds : angle 3.90882 ( 2658) glycosidic custom : bond 0.00158 ( 3) glycosidic custom : angle 0.77389 ( 9) covalent geometry : bond 0.00323 (17948) covalent geometry : angle 0.55641 (24395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13041.48 seconds wall clock time: 224 minutes 56.21 seconds (13496.21 seconds total)