Starting phenix.real_space_refine on Sun Aug 24 05:58:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vi0_43245/08_2025/8vi0_43245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vi0_43245/08_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_43245/08_2025/8vi0_43245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vi0_43245/08_2025/8vi0_43245.map" model { file = "/net/cci-nas-00/data/ceres_data/8vi0_43245/08_2025/8vi0_43245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vi0_43245/08_2025/8vi0_43245.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.39, per 1000 atoms: 0.19 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: 1.74 Conformation dependent library (CDL) restraints added in 980.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.62 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: 2.81 Time building geometry restraints manager: 2.22 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: 5.980 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- 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 : 6.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.000 ARG D 820 TYR 0.014 0.001 TYR D 270 PHE 0.009 0.001 PHE D 925 TRP 0.023 0.001 TRP A 257 HIS 0.004 0.001 HIS B 917 Details of bonding type rmsd covalent geometry : bond 0.00221 (17948) covalent geometry : angle 0.49922 (24395) hydrogen bonds : bond 0.11516 ( 898) hydrogen bonds : angle 5.13382 ( 2658) glycosidic custom : bond 0.00191 ( 3) glycosidic custom : angle 0.75257 ( 9) link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 0.88019 ( 9) *********************** 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 : 0.622 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: 0.4267 time to fit residues: 143.6722 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 : 0.535 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 816 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107573 restraints weight = 20615.972| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.25 r_work: 0.3138 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17954 Z= 0.188 Angle : 0.547 9.278 24413 Z= 0.279 Chirality : 0.044 0.178 2686 Planarity : 0.004 0.037 3042 Dihedral : 4.914 59.429 2506 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.95 % Allowed : 15.91 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.18), residues: 2151 helix: 2.00 (0.15), residues: 1178 sheet: 1.61 (0.48), residues: 131 loop : -0.71 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 921 TYR 0.016 0.001 TYR D 858 PHE 0.012 0.001 PHE B 637 TRP 0.031 0.001 TRP A 257 HIS 0.006 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00466 (17948) covalent geometry : angle 0.54625 (24395) hydrogen bonds : bond 0.04516 ( 898) hydrogen bonds : angle 4.16368 ( 2658) glycosidic custom : bond 0.00103 ( 3) glycosidic custom : angle 0.94209 ( 9) link_BETA1-4 : bond 0.00313 ( 3) link_BETA1-4 : angle 1.17943 ( 9) *********************** 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 340 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 ILE cc_start: 0.8117 (tp) cc_final: 0.7837 (pp) REVERT: A 307 GLU cc_start: 0.6334 (mp0) cc_final: 0.6069 (mp0) REVERT: A 426 GLU cc_start: 0.8676 (tp30) cc_final: 0.7863 (tp30) REVERT: A 840 TYR cc_start: 0.6718 (m-80) cc_final: 0.6289 (m-80) REVERT: B 820 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7395 (ttp80) REVERT: B 880 LYS cc_start: 0.7184 (mmtm) cc_final: 0.6899 (mmmt) REVERT: B 936 PHE cc_start: 0.7601 (m-80) cc_final: 0.7310 (m-80) REVERT: D 528 TYR cc_start: 0.7992 (m-80) cc_final: 0.7614 (m-80) REVERT: D 719 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7611 (mmmm) REVERT: D 792 ARG cc_start: 0.7540 (mpt180) cc_final: 0.7097 (mpp-170) REVERT: D 808 PRO cc_start: 0.7810 (Cg_exo) cc_final: 0.7590 (Cg_endo) REVERT: D 840 TYR cc_start: 0.6691 (m-80) cc_final: 0.6311 (m-80) REVERT: D 938 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6900 (mp) outliers start: 55 outliers final: 23 residues processed: 318 average time/residue: 0.4312 time to fit residues: 156.5350 Evaluate side-chains 288 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 405 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 982 THR 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 490 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 LEU 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 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 719 LYS Chi-restraints excluded: chain D residue 857 VAL 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 4 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 924 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.168108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111362 restraints weight = 21016.878| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.32 r_work: 0.3146 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17954 Z= 0.128 Angle : 0.506 13.302 24413 Z= 0.254 Chirality : 0.041 0.159 2686 Planarity : 0.004 0.048 3042 Dihedral : 4.386 53.703 2491 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.84 % Allowed : 17.41 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.18), residues: 2151 helix: 2.14 (0.16), residues: 1166 sheet: 1.60 (0.48), residues: 131 loop : -0.78 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 409 TYR 0.015 0.001 TYR D 858 PHE 0.010 0.001 PHE B 637 TRP 0.018 0.001 TRP A 257 HIS 0.003 0.001 HIS A 917 Details of bonding type rmsd covalent geometry : bond 0.00302 (17948) covalent geometry : angle 0.50552 (24395) hydrogen bonds : bond 0.03944 ( 898) hydrogen bonds : angle 3.98973 ( 2658) glycosidic custom : bond 0.00173 ( 3) glycosidic custom : angle 0.75351 ( 9) link_BETA1-4 : bond 0.00383 ( 3) link_BETA1-4 : angle 1.01582 ( 9) *********************** 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 329 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 920 TRP cc_start: 0.7479 (t-100) cc_final: 0.7254 (t-100) REVERT: A 924 GLN cc_start: 0.6290 (mt0) cc_final: 0.6078 (tt0) REVERT: B 259 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7663 (mppt) REVERT: B 317 ASP cc_start: 0.8037 (t0) cc_final: 0.6991 (m-30) REVERT: B 426 GLU cc_start: 0.8629 (tp30) cc_final: 0.8088 (tp30) REVERT: B 491 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7579 (ptp-110) REVERT: B 506 VAL cc_start: 0.7164 (OUTLIER) cc_final: 0.6950 (p) REVERT: B 820 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.7429 (ttp80) REVERT: B 880 LYS cc_start: 0.7206 (mmtm) cc_final: 0.6886 (mmmt) REVERT: B 921 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7104 (ttm110) REVERT: B 1020 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7203 (tp) REVERT: D 360 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7129 (mpm) REVERT: D 528 TYR cc_start: 0.7961 (m-80) cc_final: 0.7613 (m-80) REVERT: D 719 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7619 (mmmm) REVERT: D 749 LYS cc_start: 0.7553 (tptp) cc_final: 0.6986 (mtpp) REVERT: D 792 ARG cc_start: 0.7540 (mpt180) cc_final: 0.7106 (mpp-170) REVERT: D 808 PRO cc_start: 0.7797 (Cg_exo) cc_final: 0.7574 (Cg_endo) REVERT: D 860 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6383 (mt) REVERT: D 906 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6696 (mp) REVERT: D 936 PHE cc_start: 0.7929 (m-80) cc_final: 0.7644 (m-80) REVERT: D 938 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6991 (mp) outliers start: 53 outliers final: 26 residues processed: 307 average time/residue: 0.4239 time to fit residues: 149.3822 Evaluate side-chains 295 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 349 ASP Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 267 ILE 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 472 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 606 ASN 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 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 445 ILE 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 719 LYS 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 76 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 184 optimal weight: 0.1980 chunk 127 optimal weight: 0.5980 chunk 180 optimal weight: 0.0570 chunk 124 optimal weight: 0.1980 chunk 202 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 268 ASN D 291 HIS D 503 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112351 restraints weight = 20964.823| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.34 r_work: 0.3158 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17954 Z= 0.107 Angle : 0.474 9.670 24413 Z= 0.240 Chirality : 0.041 0.171 2686 Planarity : 0.004 0.035 3042 Dihedral : 4.122 52.911 2487 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.70 % Allowed : 17.62 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2151 helix: 2.23 (0.16), residues: 1167 sheet: 1.67 (0.48), residues: 131 loop : -0.76 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 820 TYR 0.015 0.001 TYR D 858 PHE 0.013 0.001 PHE B 637 TRP 0.013 0.001 TRP A 911 HIS 0.004 0.001 HIS A 917 Details of bonding type rmsd covalent geometry : bond 0.00243 (17948) covalent geometry : angle 0.47394 (24395) hydrogen bonds : bond 0.03632 ( 898) hydrogen bonds : angle 3.88063 ( 2658) glycosidic custom : bond 0.00194 ( 3) glycosidic custom : angle 0.72765 ( 9) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 1.00010 ( 9) *********************** 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 342 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7886 (t0) cc_final: 0.6969 (m-30) REVERT: B 259 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7625 (mppt) REVERT: B 317 ASP cc_start: 0.8012 (t0) cc_final: 0.6966 (m-30) REVERT: B 426 GLU cc_start: 0.8536 (tp30) cc_final: 0.7947 (tp30) REVERT: B 528 TYR cc_start: 0.7681 (m-80) cc_final: 0.7061 (m-80) REVERT: B 820 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7388 (ttp80) REVERT: B 921 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7090 (ttm110) REVERT: D 259 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7600 (mppt) REVERT: D 360 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7072 (mpm) REVERT: D 528 TYR cc_start: 0.7898 (m-80) cc_final: 0.7529 (m-80) REVERT: D 719 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7535 (mmmm) REVERT: D 749 LYS cc_start: 0.7605 (tptp) cc_final: 0.7004 (mtpp) REVERT: D 792 ARG cc_start: 0.7491 (mpt180) cc_final: 0.7054 (mpp-170) REVERT: D 808 PRO cc_start: 0.7752 (Cg_exo) cc_final: 0.7520 (Cg_endo) REVERT: D 840 TYR cc_start: 0.6676 (m-80) cc_final: 0.6423 (m-80) REVERT: D 860 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6268 (tp) REVERT: D 880 LYS cc_start: 0.7847 (mmtp) cc_final: 0.7310 (mppt) REVERT: D 906 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6539 (mp) REVERT: D 938 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6913 (mp) outliers start: 69 outliers final: 36 residues processed: 312 average time/residue: 0.4044 time to fit residues: 144.6748 Evaluate side-chains 300 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 ILE 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 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 554 LEU 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 319 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 472 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 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 361 LYS Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 554 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 203 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 94 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 922 ASN B 924 GLN D 291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111365 restraints weight = 20820.198| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.32 r_work: 0.3155 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17954 Z= 0.122 Angle : 0.496 12.269 24413 Z= 0.249 Chirality : 0.041 0.153 2686 Planarity : 0.004 0.058 3042 Dihedral : 4.114 53.315 2486 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.70 % Allowed : 17.78 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2151 helix: 2.27 (0.15), residues: 1156 sheet: 1.72 (0.49), residues: 131 loop : -0.79 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 921 TYR 0.016 0.001 TYR D 858 PHE 0.016 0.001 PHE B 637 TRP 0.017 0.001 TRP D 919 HIS 0.006 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00291 (17948) covalent geometry : angle 0.49558 (24395) hydrogen bonds : bond 0.03759 ( 898) hydrogen bonds : angle 3.87913 ( 2658) glycosidic custom : bond 0.00195 ( 3) glycosidic custom : angle 0.79127 ( 9) link_BETA1-4 : bond 0.00379 ( 3) link_BETA1-4 : angle 1.01268 ( 9) *********************** 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 339 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 270 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7935 (t0) cc_final: 0.7025 (m-30) REVERT: A 921 ARG cc_start: 0.7374 (ttm110) cc_final: 0.7126 (ttm110) REVERT: B 259 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7676 (mppt) REVERT: B 317 ASP cc_start: 0.8023 (t0) cc_final: 0.6944 (m-30) REVERT: B 426 GLU cc_start: 0.8579 (tp30) cc_final: 0.7997 (tp30) REVERT: B 506 VAL cc_start: 0.7235 (OUTLIER) cc_final: 0.7013 (p) REVERT: B 637 PHE cc_start: 0.8403 (m-10) cc_final: 0.8192 (m-10) REVERT: B 820 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7422 (ttp80) REVERT: B 880 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7627 (mppt) REVERT: B 921 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7081 (ttm110) REVERT: D 307 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: D 360 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7093 (mpm) REVERT: D 528 TYR cc_start: 0.7917 (m-80) cc_final: 0.7572 (m-80) REVERT: D 719 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7596 (mmmm) REVERT: D 792 ARG cc_start: 0.7510 (mpt180) cc_final: 0.7076 (mpp-170) REVERT: D 808 PRO cc_start: 0.7871 (Cg_exo) cc_final: 0.7646 (Cg_endo) REVERT: D 860 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6357 (mt) REVERT: D 906 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6776 (mp) REVERT: D 938 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6928 (mp) outliers start: 69 outliers final: 36 residues processed: 313 average time/residue: 0.3938 time to fit residues: 142.7177 Evaluate side-chains 302 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 628 THR Chi-restraints excluded: chain A residue 733 LEU 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 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 349 ASP 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 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 273 ILE 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 360 MET Chi-restraints excluded: chain D residue 361 LYS 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 628 THR Chi-restraints excluded: chain D residue 719 LYS 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 151 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 150 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 922 ASN B 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107683 restraints weight = 20667.013| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.25 r_work: 0.3135 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17954 Z= 0.133 Angle : 0.505 8.805 24413 Z= 0.254 Chirality : 0.041 0.154 2686 Planarity : 0.004 0.041 3042 Dihedral : 4.147 55.083 2486 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.80 % Allowed : 17.94 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.18), residues: 2151 helix: 2.28 (0.15), residues: 1157 sheet: 1.75 (0.49), residues: 131 loop : -0.80 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 820 TYR 0.016 0.001 TYR D 858 PHE 0.013 0.001 PHE B 637 TRP 0.019 0.001 TRP D 919 HIS 0.015 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00322 (17948) covalent geometry : angle 0.50440 (24395) hydrogen bonds : bond 0.03839 ( 898) hydrogen bonds : angle 3.86109 ( 2658) glycosidic custom : bond 0.00168 ( 3) glycosidic custom : angle 0.79415 ( 9) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 1.03669 ( 9) *********************** 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 335 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 264 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7933 (t0) cc_final: 0.7025 (m-30) REVERT: B 256 LEU cc_start: 0.7096 (mt) cc_final: 0.6812 (mp) REVERT: B 317 ASP cc_start: 0.8088 (t0) cc_final: 0.7011 (m-30) REVERT: B 426 GLU cc_start: 0.8589 (tp30) cc_final: 0.7985 (tp30) REVERT: B 427 TRP cc_start: 0.8954 (m-90) cc_final: 0.8737 (m-90) REVERT: B 820 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.7452 (ttp80) REVERT: B 921 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7147 (ttm110) REVERT: D 307 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: D 349 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: D 360 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7165 (mpm) REVERT: D 528 TYR cc_start: 0.7957 (m-80) cc_final: 0.7667 (m-80) REVERT: D 611 ASP cc_start: 0.8001 (m-30) cc_final: 0.6985 (t0) REVERT: D 719 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7750 (mmmm) REVERT: D 749 LYS cc_start: 0.7589 (tptp) cc_final: 0.7028 (mtpp) REVERT: D 792 ARG cc_start: 0.7511 (mpt180) cc_final: 0.7092 (mpp-170) REVERT: D 808 PRO cc_start: 0.7900 (Cg_exo) cc_final: 0.7683 (Cg_endo) REVERT: D 840 TYR cc_start: 0.6758 (m-80) cc_final: 0.6539 (m-80) REVERT: D 860 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6464 (mt) REVERT: D 906 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6681 (mp) REVERT: D 938 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6973 (mp) outliers start: 71 outliers final: 46 residues processed: 306 average time/residue: 0.4103 time to fit residues: 144.5532 Evaluate side-chains 313 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU 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 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 628 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 933 SER 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 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 617 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 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 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 554 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 207 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN B 606 ASN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110757 restraints weight = 20826.573| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.36 r_work: 0.3134 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17954 Z= 0.122 Angle : 0.503 10.986 24413 Z= 0.252 Chirality : 0.041 0.154 2686 Planarity : 0.004 0.062 3042 Dihedral : 4.145 56.643 2486 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.80 % Allowed : 18.16 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.18), residues: 2151 helix: 2.27 (0.15), residues: 1157 sheet: 1.76 (0.49), residues: 131 loop : -0.79 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 921 TYR 0.016 0.001 TYR D 858 PHE 0.017 0.001 PHE B 637 TRP 0.023 0.001 TRP D 919 HIS 0.012 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00292 (17948) covalent geometry : angle 0.50302 (24395) hydrogen bonds : bond 0.03732 ( 898) hydrogen bonds : angle 3.85564 ( 2658) glycosidic custom : bond 0.00181 ( 3) glycosidic custom : angle 0.76866 ( 9) link_BETA1-4 : bond 0.00378 ( 3) link_BETA1-4 : angle 1.02437 ( 9) *********************** 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 345 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 274 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7851 (t0) cc_final: 0.6869 (m-30) REVERT: A 596 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4931 (pp) REVERT: A 808 PRO cc_start: 0.7849 (Cg_exo) cc_final: 0.7565 (Cg_endo) REVERT: B 256 LEU cc_start: 0.6946 (mt) cc_final: 0.6664 (mp) REVERT: B 317 ASP cc_start: 0.8050 (t0) cc_final: 0.6998 (m-30) REVERT: B 360 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7838 (mpp) REVERT: B 426 GLU cc_start: 0.8534 (tp30) cc_final: 0.7926 (tp30) REVERT: B 427 TRP cc_start: 0.8936 (m-90) cc_final: 0.8663 (m-90) REVERT: B 637 PHE cc_start: 0.8433 (m-10) cc_final: 0.8205 (m-10) REVERT: B 820 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7406 (ttp80) REVERT: B 880 LYS cc_start: 0.7749 (mmmm) cc_final: 0.7387 (mmmt) REVERT: B 921 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7144 (ttm110) REVERT: D 259 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7586 (mppt) REVERT: D 349 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: D 360 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7091 (mpm) REVERT: D 426 GLU cc_start: 0.8530 (tp30) cc_final: 0.8280 (tp30) REVERT: D 528 TYR cc_start: 0.7882 (m-80) cc_final: 0.7635 (m-80) REVERT: D 719 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7564 (mmmm) REVERT: D 749 LYS cc_start: 0.7564 (tptp) cc_final: 0.6942 (mtpp) REVERT: D 792 ARG cc_start: 0.7483 (mpt180) cc_final: 0.7058 (mpp-170) REVERT: D 808 PRO cc_start: 0.7871 (Cg_exo) cc_final: 0.7658 (Cg_endo) REVERT: D 860 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6367 (mt) REVERT: D 906 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6678 (mp) REVERT: D 938 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6913 (mp) outliers start: 71 outliers final: 44 residues processed: 319 average time/residue: 0.3920 time to fit residues: 144.2876 Evaluate side-chains 316 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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 733 LEU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE 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 575 MET Chi-restraints excluded: chain B residue 617 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 977 LEU Chi-restraints excluded: chain B residue 1041 ILE 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 440 VAL 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 628 THR Chi-restraints excluded: chain D residue 719 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 141 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107300 restraints weight = 20796.247| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.33 r_work: 0.3087 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17954 Z= 0.187 Angle : 0.560 15.914 24413 Z= 0.280 Chirality : 0.043 0.176 2686 Planarity : 0.005 0.062 3042 Dihedral : 4.312 57.254 2486 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.28 % Allowed : 17.78 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2151 helix: 2.09 (0.15), residues: 1155 sheet: 1.61 (0.50), residues: 131 loop : -0.91 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 921 TYR 0.016 0.001 TYR D 858 PHE 0.020 0.001 PHE B 637 TRP 0.039 0.002 TRP A 257 HIS 0.005 0.001 HIS D 789 Details of bonding type rmsd covalent geometry : bond 0.00466 (17948) covalent geometry : angle 0.55938 (24395) hydrogen bonds : bond 0.04417 ( 898) hydrogen bonds : angle 3.98442 ( 2658) glycosidic custom : bond 0.00146 ( 3) glycosidic custom : angle 0.88761 ( 9) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 1.12886 ( 9) *********************** 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 355 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 275 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7872 (t0) cc_final: 0.6904 (m-30) REVERT: A 427 TRP cc_start: 0.9156 (m-90) cc_final: 0.8944 (m-90) REVERT: A 433 VAL cc_start: 0.7685 (t) cc_final: 0.7449 (m) REVERT: A 596 ILE cc_start: 0.5307 (OUTLIER) cc_final: 0.4957 (pp) REVERT: A 749 LYS cc_start: 0.8009 (ptmt) cc_final: 0.7363 (tptp) REVERT: A 808 PRO cc_start: 0.8006 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: A 933 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8225 (p) REVERT: A 936 PHE cc_start: 0.7670 (m-80) cc_final: 0.7225 (m-80) REVERT: B 256 LEU cc_start: 0.6978 (mt) cc_final: 0.6652 (mp) REVERT: B 259 LYS cc_start: 0.7936 (mppt) cc_final: 0.7706 (mppt) REVERT: B 317 ASP cc_start: 0.8030 (t0) cc_final: 0.6969 (m-30) REVERT: B 426 GLU cc_start: 0.8600 (tp30) cc_final: 0.7915 (tp30) REVERT: B 596 ILE cc_start: 0.5679 (OUTLIER) cc_final: 0.5254 (pp) REVERT: B 820 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7382 (ttp80) REVERT: B 880 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7462 (mmmt) REVERT: D 259 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7623 (mppt) REVERT: D 349 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: D 433 VAL cc_start: 0.7589 (t) cc_final: 0.7332 (m) REVERT: D 611 ASP cc_start: 0.8064 (m-30) cc_final: 0.7009 (t0) REVERT: D 624 ILE cc_start: 0.8736 (mt) cc_final: 0.8444 (mp) REVERT: D 792 ARG cc_start: 0.7518 (mpt180) cc_final: 0.7099 (mpp-170) REVERT: D 808 PRO cc_start: 0.7931 (Cg_exo) cc_final: 0.7692 (Cg_endo) REVERT: D 860 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6223 (mt) REVERT: D 906 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6742 (mp) REVERT: D 938 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6901 (mp) outliers start: 80 outliers final: 42 residues processed: 324 average time/residue: 0.4086 time to fit residues: 152.4320 Evaluate side-chains 313 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 866 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 933 SER 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 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER 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 617 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 935 LEU 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 291 HIS 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 440 VAL 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 628 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A 940 GLN B 606 ASN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.166197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108793 restraints weight = 20857.639| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.32 r_work: 0.3110 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17954 Z= 0.142 Angle : 0.551 13.516 24413 Z= 0.273 Chirality : 0.042 0.201 2686 Planarity : 0.005 0.074 3042 Dihedral : 4.298 58.477 2486 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.27 % Allowed : 19.50 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.18), residues: 2151 helix: 2.11 (0.15), residues: 1155 sheet: 1.56 (0.49), residues: 131 loop : -0.89 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 921 TYR 0.019 0.001 TYR A 287 PHE 0.021 0.001 PHE B 637 TRP 0.038 0.001 TRP A 257 HIS 0.006 0.001 HIS B 917 Details of bonding type rmsd covalent geometry : bond 0.00346 (17948) covalent geometry : angle 0.55013 (24395) hydrogen bonds : bond 0.04084 ( 898) hydrogen bonds : angle 3.95292 ( 2658) glycosidic custom : bond 0.00155 ( 3) glycosidic custom : angle 0.79278 ( 9) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 1.07881 ( 9) *********************** 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 329 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7848 (t0) cc_final: 0.6947 (m-30) REVERT: A 427 TRP cc_start: 0.9133 (m-90) cc_final: 0.8891 (m-90) REVERT: A 433 VAL cc_start: 0.7650 (t) cc_final: 0.7423 (m) REVERT: A 572 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8286 (mpp) REVERT: A 596 ILE cc_start: 0.5327 (OUTLIER) cc_final: 0.4980 (pp) REVERT: A 808 PRO cc_start: 0.8007 (Cg_exo) cc_final: 0.7806 (Cg_endo) REVERT: A 933 SER cc_start: 0.8481 (m) cc_final: 0.8179 (p) REVERT: B 256 LEU cc_start: 0.6963 (mt) cc_final: 0.6650 (mp) REVERT: B 259 LYS cc_start: 0.7916 (mppt) cc_final: 0.7693 (mppt) REVERT: B 317 ASP cc_start: 0.8012 (t0) cc_final: 0.6959 (m-30) REVERT: B 360 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7822 (mpp) REVERT: B 426 GLU cc_start: 0.8539 (tp30) cc_final: 0.7882 (tp30) REVERT: B 427 TRP cc_start: 0.9032 (m-90) cc_final: 0.8746 (m-90) REVERT: B 596 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5119 (pp) REVERT: B 637 PHE cc_start: 0.8485 (m-10) cc_final: 0.8263 (m-10) REVERT: B 820 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7405 (ttp80) REVERT: B 880 LYS cc_start: 0.7741 (mmmm) cc_final: 0.7477 (mmmt) REVERT: B 924 GLN cc_start: 0.6468 (mt0) cc_final: 0.6105 (tt0) REVERT: D 257 TRP cc_start: 0.7059 (p-90) cc_final: 0.6664 (p-90) REVERT: D 259 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7584 (mppt) REVERT: D 307 GLU cc_start: 0.6636 (mp0) cc_final: 0.6187 (mp0) REVERT: D 349 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: D 433 VAL cc_start: 0.7606 (t) cc_final: 0.7351 (m) REVERT: D 437 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8024 (tttm) REVERT: D 596 ILE cc_start: 0.5429 (OUTLIER) cc_final: 0.4946 (pp) REVERT: D 611 ASP cc_start: 0.8020 (m-30) cc_final: 0.6971 (t0) REVERT: D 624 ILE cc_start: 0.8711 (mt) cc_final: 0.8420 (mp) REVERT: D 792 ARG cc_start: 0.7608 (mpt180) cc_final: 0.7205 (mpp-170) REVERT: D 860 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6183 (mt) REVERT: D 906 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6666 (mp) REVERT: D 938 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6860 (mp) outliers start: 61 outliers final: 43 residues processed: 309 average time/residue: 0.3894 time to fit residues: 139.4264 Evaluate side-chains 314 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 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 906 ILE 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 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 596 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 935 LEU 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 291 HIS 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 377 VAL 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 596 ILE Chi-restraints excluded: chain D residue 628 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 198 optimal weight: 0.0370 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 185 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107480 restraints weight = 20467.970| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.25 r_work: 0.3133 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17954 Z= 0.120 Angle : 0.538 13.794 24413 Z= 0.267 Chirality : 0.042 0.215 2686 Planarity : 0.005 0.078 3042 Dihedral : 4.260 58.708 2486 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.11 % Allowed : 19.60 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.18), residues: 2151 helix: 2.16 (0.15), residues: 1155 sheet: 1.83 (0.49), residues: 127 loop : -0.87 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 921 TYR 0.019 0.001 TYR A 287 PHE 0.017 0.001 PHE B 637 TRP 0.031 0.001 TRP D 919 HIS 0.007 0.001 HIS B 917 Details of bonding type rmsd covalent geometry : bond 0.00283 (17948) covalent geometry : angle 0.53730 (24395) hydrogen bonds : bond 0.03833 ( 898) hydrogen bonds : angle 3.90110 ( 2658) glycosidic custom : bond 0.00184 ( 3) glycosidic custom : angle 0.75339 ( 9) link_BETA1-4 : bond 0.00419 ( 3) link_BETA1-4 : angle 1.05518 ( 9) ********************** 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 322 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 TRP cc_start: 0.7091 (p-90) cc_final: 0.6884 (p-90) REVERT: A 317 ASP cc_start: 0.7993 (t0) cc_final: 0.7041 (m-30) REVERT: A 427 TRP cc_start: 0.9055 (m-90) cc_final: 0.8845 (m-90) REVERT: A 596 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.5019 (pp) REVERT: A 933 SER cc_start: 0.8511 (m) cc_final: 0.8215 (p) REVERT: B 256 LEU cc_start: 0.7090 (mt) cc_final: 0.6773 (mp) REVERT: B 317 ASP cc_start: 0.7980 (t0) cc_final: 0.6886 (m-30) REVERT: B 360 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7881 (mpp) REVERT: B 426 GLU cc_start: 0.8587 (tp30) cc_final: 0.7949 (tp30) REVERT: B 427 TRP cc_start: 0.9066 (m-90) cc_final: 0.8781 (m-90) REVERT: B 596 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5163 (pp) REVERT: B 637 PHE cc_start: 0.8478 (m-10) cc_final: 0.8231 (m-10) REVERT: B 820 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7448 (ttp80) REVERT: B 880 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7541 (mmmt) REVERT: B 924 GLN cc_start: 0.6643 (mt0) cc_final: 0.6101 (tt0) REVERT: D 257 TRP cc_start: 0.7022 (p-90) cc_final: 0.6710 (p-90) REVERT: D 259 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7635 (mppt) REVERT: D 307 GLU cc_start: 0.6700 (mp0) cc_final: 0.6242 (mp0) REVERT: D 349 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: D 437 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8112 (tttm) REVERT: D 611 ASP cc_start: 0.8064 (m-30) cc_final: 0.6982 (t0) REVERT: D 624 ILE cc_start: 0.8755 (mt) cc_final: 0.8485 (mp) REVERT: D 792 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7246 (mpp-170) REVERT: D 860 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6279 (mt) REVERT: D 906 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6735 (mp) REVERT: D 938 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6935 (mp) outliers start: 58 outliers final: 41 residues processed: 306 average time/residue: 0.3903 time to fit residues: 138.5048 Evaluate side-chains 304 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 866 ILE Chi-restraints excluded: chain A residue 906 ILE 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 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 617 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE 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 377 VAL 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 628 THR Chi-restraints excluded: chain D residue 733 LEU 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 906 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 27 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 chunk 198 optimal weight: 0.0040 chunk 173 optimal weight: 0.0770 overall best weight: 0.4150 ------------------------------------------------------------------------------- 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 ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.167215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110784 restraints weight = 20856.824| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.30 r_work: 0.3150 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17954 Z= 0.118 Angle : 0.539 13.831 24413 Z= 0.266 Chirality : 0.041 0.220 2686 Planarity : 0.004 0.076 3042 Dihedral : 4.216 58.847 2486 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.16 % Allowed : 19.82 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.18), residues: 2151 helix: 2.15 (0.15), residues: 1160 sheet: 1.85 (0.49), residues: 127 loop : -0.88 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 921 TYR 0.020 0.001 TYR A 287 PHE 0.015 0.001 PHE B 637 TRP 0.033 0.001 TRP A 911 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00276 (17948) covalent geometry : angle 0.53867 (24395) hydrogen bonds : bond 0.03719 ( 898) hydrogen bonds : angle 3.87565 ( 2658) glycosidic custom : bond 0.00150 ( 3) glycosidic custom : angle 0.75762 ( 9) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 1.07077 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.33 seconds wall clock time: 97 minutes 56.18 seconds (5876.18 seconds total)