Starting phenix.real_space_refine on Thu Jul 31 17:56:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7air_11803/07_2025/7air_11803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7air_11803/07_2025/7air_11803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2025/7air_11803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2025/7air_11803.map" model { file = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2025/7air_11803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2025/7air_11803.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 96 5.16 5 C 8760 2.51 5 N 2221 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13504 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 6707 Classifications: {'peptide': 885} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 38, 'TRANS': 846} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 866, 6623 Classifications: {'peptide': 866} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 37, 'TRANS': 828} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.87, per 1000 atoms: 0.66 Number of scatterers: 13504 At special positions: 0 Unit cell: (108.8, 110.5, 159.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 5 15.00 O 2422 8.00 N 2221 7.00 C 8760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.05 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.04 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 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 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1101 " - " ASN B 361 " " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.7 seconds 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3222 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 62.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 120 through 133 removed outlier: 5.842A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 134 through 141 removed outlier: 4.710A pdb=" N PHE A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 177 removed outlier: 6.509A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 227 removed outlier: 4.311A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Proline residue: A 195 - end of helix removed outlier: 3.866A pdb=" N TYR A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 269 Processing helix chain 'A' and resid 269 through 301 removed outlier: 5.535A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.876A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.957A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.703A pdb=" N GLY A 437 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 504 through 536 removed outlier: 4.211A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.925A pdb=" N LEU A 542 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.637A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 661 Processing helix chain 'A' and resid 664 through 682 removed outlier: 4.080A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.827A pdb=" N THR A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.521A pdb=" N ALA A 742 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 780 Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.598A pdb=" N LYS A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.656A pdb=" N TYR A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 888 through 903 removed outlier: 3.792A pdb=" N HIS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 941 Processing helix chain 'A' and resid 1012 through 1033 removed outlier: 4.114A pdb=" N ARG A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A1019 " --> pdb=" O ASN A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 3.633A pdb=" N THR A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 133 removed outlier: 5.930A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.697A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 177 removed outlier: 6.862A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.559A pdb=" N LEU B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 269 Processing helix chain 'B' and resid 269 through 301 removed outlier: 5.575A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.825A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.933A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.817A pdb=" N LEU B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 446 through 477 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 494 through 498 removed outlier: 3.514A pdb=" N THR B 498 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 536 removed outlier: 4.302A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.945A pdb=" N LEU B 542 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 545 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 570 Processing helix chain 'B' and resid 573 through 602 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.727A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 661 Processing helix chain 'B' and resid 664 through 682 removed outlier: 4.264A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 3.674A pdb=" N THR B 713 " --> pdb=" O PRO B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.626A pdb=" N ALA B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 780 Processing helix chain 'B' and resid 805 through 820 removed outlier: 3.579A pdb=" N LYS B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 removed outlier: 3.540A pdb=" N TYR B 834 " --> pdb=" O ILE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 867 Proline residue: B 862 - end of helix Processing helix chain 'B' and resid 868 through 872 Processing helix chain 'B' and resid 887 through 903 removed outlier: 3.587A pdb=" N HIS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 926 removed outlier: 5.324A pdb=" N ALA B 920 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR B 921 " --> pdb=" O ASP B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1033 removed outlier: 3.548A pdb=" N MET B1019 " --> pdb=" O ASN B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 3.618A pdb=" N THR B1064 " --> pdb=" O LEU B1060 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.573A pdb=" N LEU A 310 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767 removed outlier: 6.658A pdb=" N THR A 725 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN A 763 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL A 727 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 765 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER A 729 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA A 767 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE A 731 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 728 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 695 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 791 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A1072 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LEU A1040 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP A 847 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ASN A1042 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 846 " --> pdb=" O ARG A 877 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE A 879 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A 848 " --> pdb=" O PHE A 879 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 907 " --> pdb=" O MET A 876 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.751A pdb=" N LEU A 783 " --> pdb=" O MET A 786 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.546A pdb=" N VAL B 307 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA7, first strand: chain 'B' and resid 761 through 762 removed outlier: 3.571A pdb=" N ILE B 726 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 791 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B1072 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU B1040 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 847 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B1042 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 846 " --> pdb=" O ARG B 877 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE B 879 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 848 " --> pdb=" O PHE B 879 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET B 876 " --> pdb=" O GLU B 907 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU B 909 " --> pdb=" O MET B 876 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE B 878 " --> pdb=" O GLU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 730 through 732 Processing sheet with id=AA9, first strand: chain 'B' and resid 782 through 783 769 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4231 1.35 - 1.47: 3518 1.47 - 1.60: 5903 1.60 - 1.72: 12 1.72 - 1.85: 152 Bond restraints: 13816 Sorted by residual: bond pdb=" C4 ATP A1201 " pdb=" C5 ATP A1201 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP B1102 " pdb=" C5 ATP B1102 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C5 ATP A1201 " pdb=" C6 ATP A1201 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.80e+01 bond pdb=" O1B ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 1.477 1.610 -0.133 2.20e-02 2.07e+03 3.66e+01 bond pdb=" O1B ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 1.477 1.608 -0.131 2.20e-02 2.07e+03 3.52e+01 ... (remaining 13811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 18364 2.61 - 5.23: 383 5.23 - 7.84: 64 7.84 - 10.46: 14 10.46 - 13.07: 4 Bond angle restraints: 18829 Sorted by residual: angle pdb=" PA ATP B1102 " pdb=" O3A ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 136.83 123.96 12.87 1.00e+00 1.00e+00 1.66e+02 angle pdb=" PA ATP A1201 " pdb=" O3A ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 136.83 125.68 11.15 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C5 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N3 ATP A1201 " ideal model delta sigma weight residual 126.80 118.27 8.53 1.00e+00 1.00e+00 7.28e+01 angle pdb=" C5 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N3 ATP B1102 " ideal model delta sigma weight residual 126.80 118.82 7.98 1.00e+00 1.00e+00 6.38e+01 angle pdb=" N3 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N9 ATP A1201 " ideal model delta sigma weight residual 127.04 135.13 -8.09 1.15e+00 7.59e-01 4.96e+01 ... (remaining 18824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 7419 21.80 - 43.61: 691 43.61 - 65.41: 115 65.41 - 87.22: 22 87.22 - 109.02: 13 Dihedral angle restraints: 8260 sinusoidal: 3235 harmonic: 5025 Sorted by residual: dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 142.37 -49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual 93.00 136.22 -43.22 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.69 109.02 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1615 0.053 - 0.105: 512 0.105 - 0.158: 103 0.158 - 0.211: 7 0.211 - 0.263: 2 Chirality restraints: 2239 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.30 -0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 2236 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LEU A 137 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 137 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 138 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1026 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASN A1026 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN A1026 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A1027 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 121 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LEU A 121 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 121 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 122 " -0.013 2.00e-02 2.50e+03 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2709 2.76 - 3.30: 13078 3.30 - 3.83: 21217 3.83 - 4.37: 22595 4.37 - 4.90: 41575 Nonbonded interactions: 101174 Sorted by model distance: nonbonded pdb=" OG1 THR A 120 " pdb=" OG SER A 450 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A 430 " pdb=" OH TYR A 466 " model vdw 2.235 3.040 nonbonded pdb=" O PRO B 605 " pdb=" NH2 ARG B 608 " model vdw 2.251 3.120 nonbonded pdb=" O SER B 780 " pdb=" OG SER B 780 " model vdw 2.260 3.040 nonbonded pdb=" O GLY A 479 " pdb=" NH2 ARG A 483 " model vdw 2.262 3.120 ... (remaining 101169 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 116 through 233 or resid 244 through 444 or (resid 445 and \ (name N or name CA or name C or name O or name CB )) or resid 446 through 611 o \ r (resid 612 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 13 through 733 or resid 735 through 926 or resid 1014 through 1015 or (resid 101 \ 6 through 1017 and (name N or name CA or name C or name O or name CB )) or resid \ 1018 through 1081)) selection = (chain 'B' and (resid 116 through 733 or resid 735 through 881 or resid 887 thro \ ugh 899 or (resid 900 through 901 and (name N or name CA or name C or name O or \ name CB )) or resid 902 through 914 or (resid 915 through 926 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1014 through 1081)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.140 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.008 0.133 13831 Z= 0.408 Angle : 0.980 13.073 18868 Z= 0.532 Chirality : 0.051 0.263 2239 Planarity : 0.005 0.045 2322 Dihedral : 17.147 109.020 5020 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.14 % Allowed : 20.74 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1732 helix: 0.45 (0.16), residues: 971 sheet: -2.20 (0.39), residues: 136 loop : -2.70 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 381 HIS 0.011 0.002 HIS A 853 PHE 0.024 0.002 PHE A 611 TYR 0.035 0.002 TYR A 356 ARG 0.004 0.001 ARG A 710 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 4) link_NAG-ASN : angle 2.64074 ( 12) link_BETA1-4 : bond 0.00417 ( 5) link_BETA1-4 : angle 3.86845 ( 15) hydrogen bonds : bond 0.16054 ( 769) hydrogen bonds : angle 5.51862 ( 2226) SS BOND : bond 0.00723 ( 6) SS BOND : angle 3.97140 ( 12) covalent geometry : bond 0.00848 (13816) covalent geometry : angle 0.96761 (18829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 CYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7616 (m) REVERT: A 704 LEU cc_start: 0.8446 (mt) cc_final: 0.8093 (tt) REVERT: A 777 LEU cc_start: 0.8123 (tp) cc_final: 0.7788 (tp) REVERT: A 879 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.5772 (t80) REVERT: B 879 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6841 (m-80) outliers start: 16 outliers final: 3 residues processed: 334 average time/residue: 0.2546 time to fit residues: 122.9788 Evaluate side-chains 166 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 879 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 344 HIS A 615 HIS A 655 GLN A 717 GLN A 732 GLN A 747 GLN A 751 ASN A 853 HIS A 868 HIS B 131 ASN B 152 GLN B 250 ASN B 344 HIS B 521 GLN B 655 GLN B 732 GLN B 751 ASN B 853 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.111598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.084044 restraints weight = 41226.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.087242 restraints weight = 18810.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.088790 restraints weight = 10490.599| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13831 Z= 0.251 Angle : 0.774 10.419 18868 Z= 0.383 Chirality : 0.046 0.322 2239 Planarity : 0.005 0.051 2322 Dihedral : 9.890 84.458 2134 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.29 % Allowed : 22.68 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1732 helix: 1.42 (0.17), residues: 974 sheet: -1.55 (0.42), residues: 135 loop : -2.36 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 849 HIS 0.006 0.002 HIS A 845 PHE 0.020 0.002 PHE A 714 TYR 0.016 0.001 TYR B 411 ARG 0.008 0.001 ARG B 903 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 4) link_NAG-ASN : angle 2.21572 ( 12) link_BETA1-4 : bond 0.00618 ( 5) link_BETA1-4 : angle 3.60695 ( 15) hydrogen bonds : bond 0.05965 ( 769) hydrogen bonds : angle 4.54368 ( 2226) SS BOND : bond 0.01233 ( 6) SS BOND : angle 1.93600 ( 12) covalent geometry : bond 0.00565 (13816) covalent geometry : angle 0.76471 (18829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 176 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: A 542 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8793 (pp) REVERT: A 593 ASN cc_start: 0.9108 (m-40) cc_final: 0.8703 (t0) REVERT: A 623 MET cc_start: 0.8899 (ttp) cc_final: 0.8674 (ttm) REVERT: A 643 LEU cc_start: 0.8805 (tt) cc_final: 0.8592 (mm) REVERT: A 704 LEU cc_start: 0.9209 (mt) cc_final: 0.8612 (tt) REVERT: A 876 MET cc_start: 0.7944 (ttt) cc_final: 0.7686 (tmm) REVERT: B 165 LEU cc_start: 0.8351 (tp) cc_final: 0.8121 (tt) REVERT: B 630 MET cc_start: 0.8821 (ttp) cc_final: 0.8530 (mtp) REVERT: B 763 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8454 (tp-100) outliers start: 74 outliers final: 41 residues processed: 228 average time/residue: 0.2038 time to fit residues: 73.5769 Evaluate side-chains 193 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 632 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 147 optimal weight: 0.0070 chunk 140 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.113879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.086954 restraints weight = 41038.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090172 restraints weight = 18060.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.091894 restraints weight = 10118.853| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13831 Z= 0.145 Angle : 0.658 10.037 18868 Z= 0.319 Chirality : 0.043 0.312 2239 Planarity : 0.004 0.047 2322 Dihedral : 8.322 72.997 2128 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.36 % Allowed : 24.11 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1732 helix: 1.88 (0.17), residues: 987 sheet: -1.18 (0.43), residues: 134 loop : -2.05 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 501 HIS 0.005 0.001 HIS B 845 PHE 0.017 0.001 PHE B 541 TYR 0.009 0.001 TYR B 292 ARG 0.005 0.000 ARG B 903 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 2.14504 ( 12) link_BETA1-4 : bond 0.00722 ( 5) link_BETA1-4 : angle 3.35485 ( 15) hydrogen bonds : bond 0.04990 ( 769) hydrogen bonds : angle 4.15707 ( 2226) SS BOND : bond 0.00622 ( 6) SS BOND : angle 2.06787 ( 12) covalent geometry : bond 0.00325 (13816) covalent geometry : angle 0.64710 (18829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8749 (pp) REVERT: A 563 LEU cc_start: 0.8430 (mp) cc_final: 0.7937 (tt) REVERT: A 633 SER cc_start: 0.9103 (m) cc_final: 0.8889 (p) REVERT: A 643 LEU cc_start: 0.8829 (tt) cc_final: 0.8588 (mm) REVERT: A 647 MET cc_start: 0.7791 (tmm) cc_final: 0.7584 (tmm) REVERT: A 704 LEU cc_start: 0.9178 (mt) cc_final: 0.8604 (tp) REVERT: B 122 MET cc_start: 0.7603 (ttt) cc_final: 0.6822 (tmm) REVERT: B 251 MET cc_start: 0.8805 (ttm) cc_final: 0.8542 (ttm) REVERT: B 763 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8464 (tp-100) REVERT: B 1043 MET cc_start: 0.9345 (ptp) cc_final: 0.9047 (ptp) outliers start: 61 outliers final: 37 residues processed: 218 average time/residue: 0.2061 time to fit residues: 70.8521 Evaluate side-chains 195 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 861 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 44 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.114257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.086817 restraints weight = 40875.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.089943 restraints weight = 20911.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091755 restraints weight = 11353.049| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13831 Z= 0.135 Angle : 0.627 10.108 18868 Z= 0.302 Chirality : 0.042 0.281 2239 Planarity : 0.004 0.041 2322 Dihedral : 7.637 73.495 2126 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.93 % Allowed : 25.54 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1732 helix: 2.05 (0.17), residues: 987 sheet: -1.01 (0.42), residues: 136 loop : -1.82 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.004 0.001 HIS B 394 PHE 0.017 0.001 PHE A 541 TYR 0.009 0.001 TYR B 292 ARG 0.004 0.000 ARG B 903 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 4) link_NAG-ASN : angle 2.16562 ( 12) link_BETA1-4 : bond 0.00665 ( 5) link_BETA1-4 : angle 3.12145 ( 15) hydrogen bonds : bond 0.04621 ( 769) hydrogen bonds : angle 4.07199 ( 2226) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.91068 ( 12) covalent geometry : bond 0.00301 (13816) covalent geometry : angle 0.61760 (18829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8722 (pp) REVERT: A 593 ASN cc_start: 0.9065 (m-40) cc_final: 0.8811 (t0) REVERT: A 633 SER cc_start: 0.8977 (m) cc_final: 0.8771 (p) REVERT: A 643 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 647 MET cc_start: 0.7771 (tmm) cc_final: 0.7517 (tmm) REVERT: A 704 LEU cc_start: 0.9172 (mt) cc_final: 0.8626 (tp) REVERT: A 756 GLU cc_start: 0.8841 (tp30) cc_final: 0.8458 (tm-30) REVERT: A 809 LYS cc_start: 0.8764 (pttt) cc_final: 0.8504 (mtmt) REVERT: B 122 MET cc_start: 0.7646 (ttt) cc_final: 0.6915 (tmm) REVERT: B 144 MET cc_start: 0.8443 (tpp) cc_final: 0.8240 (tpp) REVERT: B 591 PHE cc_start: 0.8638 (m-80) cc_final: 0.8370 (m-80) REVERT: B 623 MET cc_start: 0.8615 (ttp) cc_final: 0.8331 (ttp) REVERT: B 763 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8477 (tp-100) outliers start: 55 outliers final: 38 residues processed: 208 average time/residue: 0.2047 time to fit residues: 67.3800 Evaluate side-chains 195 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 139 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN B 379 ASN B 868 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.115188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.087860 restraints weight = 40904.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.091140 restraints weight = 18624.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.092459 restraints weight = 10332.068| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13831 Z= 0.115 Angle : 0.605 10.227 18868 Z= 0.290 Chirality : 0.041 0.276 2239 Planarity : 0.003 0.037 2322 Dihedral : 7.219 73.679 2124 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.01 % Allowed : 25.46 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1732 helix: 2.23 (0.17), residues: 980 sheet: -0.83 (0.46), residues: 124 loop : -1.62 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 143 HIS 0.004 0.001 HIS B 776 PHE 0.019 0.001 PHE B 280 TYR 0.007 0.001 TYR A 649 ARG 0.005 0.000 ARG B 903 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 4) link_NAG-ASN : angle 2.06783 ( 12) link_BETA1-4 : bond 0.00564 ( 5) link_BETA1-4 : angle 2.76215 ( 15) hydrogen bonds : bond 0.04262 ( 769) hydrogen bonds : angle 3.94931 ( 2226) SS BOND : bond 0.00391 ( 6) SS BOND : angle 1.60635 ( 12) covalent geometry : bond 0.00249 (13816) covalent geometry : angle 0.59697 (18829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 593 ASN cc_start: 0.9047 (m-40) cc_final: 0.8792 (t0) REVERT: A 633 SER cc_start: 0.8904 (m) cc_final: 0.8688 (p) REVERT: A 643 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8557 (mm) REVERT: A 647 MET cc_start: 0.7721 (tmm) cc_final: 0.7446 (tmm) REVERT: A 704 LEU cc_start: 0.9156 (mt) cc_final: 0.8617 (tp) REVERT: A 753 MET cc_start: 0.9432 (ttm) cc_final: 0.9227 (ttm) REVERT: B 122 MET cc_start: 0.7804 (ttt) cc_final: 0.7047 (tmm) REVERT: B 623 MET cc_start: 0.8626 (ttp) cc_final: 0.8381 (ttp) REVERT: B 763 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8456 (tp-100) REVERT: B 1032 ARG cc_start: 0.8893 (tpm170) cc_final: 0.8624 (tpm170) REVERT: B 1063 LEU cc_start: 0.9793 (tp) cc_final: 0.9470 (mp) outliers start: 56 outliers final: 38 residues processed: 206 average time/residue: 0.2238 time to fit residues: 71.8175 Evaluate side-chains 198 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 73 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 63 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.114557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.087607 restraints weight = 41644.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089707 restraints weight = 17410.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091108 restraints weight = 10734.006| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13831 Z= 0.131 Angle : 0.602 10.235 18868 Z= 0.293 Chirality : 0.041 0.283 2239 Planarity : 0.003 0.037 2322 Dihedral : 7.074 74.638 2124 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.22 % Allowed : 25.75 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1732 helix: 2.34 (0.17), residues: 968 sheet: -0.54 (0.47), residues: 124 loop : -1.50 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.003 0.001 HIS A 788 PHE 0.018 0.001 PHE A 714 TYR 0.008 0.001 TYR B 466 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 4) link_NAG-ASN : angle 1.92166 ( 12) link_BETA1-4 : bond 0.00499 ( 5) link_BETA1-4 : angle 2.44718 ( 15) hydrogen bonds : bond 0.04284 ( 769) hydrogen bonds : angle 3.91356 ( 2226) SS BOND : bond 0.00388 ( 6) SS BOND : angle 1.58103 ( 12) covalent geometry : bond 0.00294 (13816) covalent geometry : angle 0.59489 (18829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8667 (pp) REVERT: A 593 ASN cc_start: 0.9039 (m-40) cc_final: 0.8791 (t0) REVERT: A 623 MET cc_start: 0.9142 (tmm) cc_final: 0.8942 (tmm) REVERT: A 633 SER cc_start: 0.8911 (m) cc_final: 0.8693 (p) REVERT: A 643 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 647 MET cc_start: 0.7727 (tmm) cc_final: 0.7428 (tmm) REVERT: A 704 LEU cc_start: 0.9149 (mt) cc_final: 0.8601 (tp) REVERT: A 891 MET cc_start: 0.9057 (tpt) cc_final: 0.8374 (mmm) REVERT: B 122 MET cc_start: 0.7923 (ttt) cc_final: 0.7203 (tmm) REVERT: B 251 MET cc_start: 0.8671 (ttm) cc_final: 0.8103 (tpp) REVERT: B 297 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8041 (mptt) REVERT: B 623 MET cc_start: 0.8666 (ttp) cc_final: 0.8391 (ttp) REVERT: B 630 MET cc_start: 0.8915 (tpp) cc_final: 0.8688 (tpp) REVERT: B 763 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8485 (tp-100) REVERT: B 813 ASP cc_start: 0.9132 (m-30) cc_final: 0.8636 (m-30) REVERT: B 876 MET cc_start: 0.8515 (ttp) cc_final: 0.8056 (ttp) REVERT: B 1032 ARG cc_start: 0.8877 (tpm170) cc_final: 0.8615 (tpm170) REVERT: B 1063 LEU cc_start: 0.9801 (tp) cc_final: 0.9477 (mp) outliers start: 59 outliers final: 40 residues processed: 205 average time/residue: 0.2137 time to fit residues: 68.4296 Evaluate side-chains 204 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085944 restraints weight = 41667.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.088079 restraints weight = 17586.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089507 restraints weight = 10821.407| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13831 Z= 0.178 Angle : 0.644 10.272 18868 Z= 0.314 Chirality : 0.042 0.284 2239 Planarity : 0.004 0.041 2322 Dihedral : 7.092 77.515 2124 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.51 % Allowed : 25.18 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1732 helix: 2.27 (0.17), residues: 977 sheet: -0.60 (0.46), residues: 124 loop : -1.44 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.004 0.001 HIS B 788 PHE 0.017 0.001 PHE B 280 TYR 0.010 0.001 TYR B 292 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 4) link_NAG-ASN : angle 1.91242 ( 12) link_BETA1-4 : bond 0.00425 ( 5) link_BETA1-4 : angle 2.34316 ( 15) hydrogen bonds : bond 0.04554 ( 769) hydrogen bonds : angle 3.99524 ( 2226) SS BOND : bond 0.00481 ( 6) SS BOND : angle 1.68713 ( 12) covalent geometry : bond 0.00403 (13816) covalent geometry : angle 0.63853 (18829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 158 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8724 (pp) REVERT: A 593 ASN cc_start: 0.9069 (m-40) cc_final: 0.8789 (t0) REVERT: A 623 MET cc_start: 0.9209 (tmm) cc_final: 0.8808 (tmm) REVERT: A 633 SER cc_start: 0.9011 (m) cc_final: 0.8783 (p) REVERT: A 643 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 647 MET cc_start: 0.7761 (tmm) cc_final: 0.7448 (tmm) REVERT: B 122 MET cc_start: 0.8003 (ttt) cc_final: 0.7337 (tmm) REVERT: B 251 MET cc_start: 0.8656 (ttm) cc_final: 0.8223 (tpp) REVERT: B 297 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8091 (mptt) REVERT: B 623 MET cc_start: 0.8669 (ttp) cc_final: 0.8357 (ttp) REVERT: B 630 MET cc_start: 0.8870 (tpp) cc_final: 0.8624 (tpp) REVERT: B 875 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7626 (ttp-110) REVERT: B 876 MET cc_start: 0.8470 (ttp) cc_final: 0.8007 (ttp) REVERT: B 1032 ARG cc_start: 0.8865 (tpm170) cc_final: 0.8612 (tpm170) REVERT: B 1063 LEU cc_start: 0.9802 (tp) cc_final: 0.9499 (mp) outliers start: 77 outliers final: 56 residues processed: 219 average time/residue: 0.2181 time to fit residues: 73.5995 Evaluate side-chains 215 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 155 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 875 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 21 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 157 optimal weight: 8.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.115210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.087856 restraints weight = 41112.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091103 restraints weight = 19147.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.093391 restraints weight = 10634.096| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13831 Z= 0.116 Angle : 0.613 10.038 18868 Z= 0.294 Chirality : 0.041 0.280 2239 Planarity : 0.004 0.042 2322 Dihedral : 6.862 76.768 2124 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.36 % Allowed : 27.04 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1732 helix: 2.36 (0.17), residues: 969 sheet: -0.32 (0.47), residues: 123 loop : -1.35 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 143 HIS 0.004 0.001 HIS A 776 PHE 0.017 0.001 PHE A 714 TYR 0.007 0.001 TYR B 636 ARG 0.006 0.000 ARG B1074 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 4) link_NAG-ASN : angle 2.00478 ( 12) link_BETA1-4 : bond 0.00538 ( 5) link_BETA1-4 : angle 2.15675 ( 15) hydrogen bonds : bond 0.04178 ( 769) hydrogen bonds : angle 3.88663 ( 2226) SS BOND : bond 0.01112 ( 6) SS BOND : angle 1.59246 ( 12) covalent geometry : bond 0.00249 (13816) covalent geometry : angle 0.60706 (18829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9142 (mt) REVERT: A 542 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8657 (pp) REVERT: A 593 ASN cc_start: 0.9021 (m-40) cc_final: 0.8771 (t0) REVERT: A 623 MET cc_start: 0.9195 (tmm) cc_final: 0.8916 (tmm) REVERT: A 643 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8555 (mm) REVERT: A 647 MET cc_start: 0.7745 (tmm) cc_final: 0.7436 (tmm) REVERT: A 704 LEU cc_start: 0.9107 (mt) cc_final: 0.8841 (pp) REVERT: A 809 LYS cc_start: 0.8777 (pttt) cc_final: 0.8545 (pttt) REVERT: B 122 MET cc_start: 0.8020 (ttt) cc_final: 0.7232 (tmm) REVERT: B 251 MET cc_start: 0.8651 (ttm) cc_final: 0.8102 (tpp) REVERT: B 623 MET cc_start: 0.8742 (ttp) cc_final: 0.8445 (ttp) REVERT: B 630 MET cc_start: 0.8844 (tpp) cc_final: 0.8643 (tpp) REVERT: B 813 ASP cc_start: 0.9143 (m-30) cc_final: 0.8657 (m-30) REVERT: B 876 MET cc_start: 0.8464 (ttp) cc_final: 0.8112 (ttp) REVERT: B 1063 LEU cc_start: 0.9799 (tp) cc_final: 0.9485 (mp) outliers start: 47 outliers final: 36 residues processed: 201 average time/residue: 0.2265 time to fit residues: 73.3540 Evaluate side-chains 197 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A1026 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN B 776 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.115591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088295 restraints weight = 40563.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.091985 restraints weight = 19151.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.093221 restraints weight = 9870.152| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13831 Z= 0.114 Angle : 0.609 10.032 18868 Z= 0.292 Chirality : 0.041 0.277 2239 Planarity : 0.004 0.040 2322 Dihedral : 6.754 75.563 2124 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.43 % Allowed : 27.54 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1732 helix: 2.33 (0.17), residues: 969 sheet: -0.17 (0.47), residues: 123 loop : -1.29 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 808 HIS 0.009 0.001 HIS B 776 PHE 0.013 0.001 PHE A 541 TYR 0.007 0.001 TYR A 649 ARG 0.010 0.000 ARG B1032 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 4) link_NAG-ASN : angle 2.05441 ( 12) link_BETA1-4 : bond 0.00474 ( 5) link_BETA1-4 : angle 2.03293 ( 15) hydrogen bonds : bond 0.04054 ( 769) hydrogen bonds : angle 3.87209 ( 2226) SS BOND : bond 0.00663 ( 6) SS BOND : angle 1.77614 ( 12) covalent geometry : bond 0.00251 (13816) covalent geometry : angle 0.60257 (18829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9121 (mt) REVERT: A 542 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8675 (pp) REVERT: A 587 MET cc_start: 0.8171 (ttp) cc_final: 0.7960 (ttm) REVERT: A 593 ASN cc_start: 0.9003 (m-40) cc_final: 0.8763 (t0) REVERT: A 623 MET cc_start: 0.9212 (tmm) cc_final: 0.8854 (tmm) REVERT: A 647 MET cc_start: 0.7768 (tmm) cc_final: 0.7468 (tmm) REVERT: A 704 LEU cc_start: 0.9099 (mt) cc_final: 0.8824 (pp) REVERT: A 809 LYS cc_start: 0.8762 (pttt) cc_final: 0.7971 (pttt) REVERT: A 813 ASP cc_start: 0.8909 (m-30) cc_final: 0.8385 (m-30) REVERT: A 1057 MET cc_start: 0.9639 (tpt) cc_final: 0.9339 (tpt) REVERT: B 122 MET cc_start: 0.7964 (ttt) cc_final: 0.7117 (tmm) REVERT: B 251 MET cc_start: 0.8715 (ttm) cc_final: 0.8172 (tpp) REVERT: B 309 MET cc_start: 0.8107 (mmm) cc_final: 0.7806 (mmm) REVERT: B 488 ASP cc_start: 0.7670 (m-30) cc_final: 0.6485 (t70) REVERT: B 623 MET cc_start: 0.8708 (ttp) cc_final: 0.8378 (ttp) REVERT: B 813 ASP cc_start: 0.9152 (m-30) cc_final: 0.8662 (m-30) REVERT: B 875 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7668 (ttp-110) REVERT: B 876 MET cc_start: 0.8461 (ttp) cc_final: 0.8084 (ttp) REVERT: B 1063 LEU cc_start: 0.9799 (tp) cc_final: 0.9486 (mp) outliers start: 48 outliers final: 36 residues processed: 204 average time/residue: 0.1945 time to fit residues: 63.3597 Evaluate side-chains 193 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 875 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 150 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.086069 restraints weight = 41612.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.088413 restraints weight = 17706.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.090717 restraints weight = 10832.627| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13831 Z= 0.152 Angle : 0.638 10.136 18868 Z= 0.310 Chirality : 0.042 0.279 2239 Planarity : 0.004 0.041 2322 Dihedral : 6.794 77.690 2124 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.15 % Allowed : 28.11 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1732 helix: 2.27 (0.17), residues: 972 sheet: -0.18 (0.46), residues: 125 loop : -1.25 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 143 HIS 0.004 0.001 HIS A 788 PHE 0.022 0.001 PHE B 280 TYR 0.010 0.001 TYR B 292 ARG 0.008 0.000 ARG B1032 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 4) link_NAG-ASN : angle 2.02430 ( 12) link_BETA1-4 : bond 0.00445 ( 5) link_BETA1-4 : angle 1.97788 ( 15) hydrogen bonds : bond 0.04354 ( 769) hydrogen bonds : angle 3.93011 ( 2226) SS BOND : bond 0.00663 ( 6) SS BOND : angle 1.92709 ( 12) covalent geometry : bond 0.00347 (13816) covalent geometry : angle 0.63264 (18829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8718 (pp) REVERT: A 593 ASN cc_start: 0.9026 (m-40) cc_final: 0.8764 (t0) REVERT: A 623 MET cc_start: 0.9256 (tmm) cc_final: 0.8920 (tmm) REVERT: A 647 MET cc_start: 0.7743 (tmm) cc_final: 0.7423 (tmm) REVERT: A 704 LEU cc_start: 0.9090 (mt) cc_final: 0.8820 (pp) REVERT: A 809 LYS cc_start: 0.8773 (pttt) cc_final: 0.8180 (pttt) REVERT: A 813 ASP cc_start: 0.8913 (m-30) cc_final: 0.8377 (m-30) REVERT: A 1057 MET cc_start: 0.9623 (tpt) cc_final: 0.9323 (tpt) REVERT: B 122 MET cc_start: 0.7924 (ttt) cc_final: 0.7688 (tpp) REVERT: B 171 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7722 (ttm) REVERT: B 251 MET cc_start: 0.8709 (ttm) cc_final: 0.8197 (tpp) REVERT: B 488 ASP cc_start: 0.7716 (m-30) cc_final: 0.6547 (t70) REVERT: B 623 MET cc_start: 0.8768 (ttp) cc_final: 0.8445 (ttp) REVERT: B 813 ASP cc_start: 0.9150 (m-30) cc_final: 0.8665 (m-30) REVERT: B 875 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7644 (ttp80) REVERT: B 876 MET cc_start: 0.8454 (ttp) cc_final: 0.8086 (ttp) REVERT: B 1063 LEU cc_start: 0.9807 (tp) cc_final: 0.9506 (mp) outliers start: 44 outliers final: 39 residues processed: 192 average time/residue: 0.2046 time to fit residues: 62.4518 Evaluate side-chains 195 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 875 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 29 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 22 optimal weight: 0.0000 chunk 100 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.110375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084072 restraints weight = 39591.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.087112 restraints weight = 18246.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.089149 restraints weight = 11320.050| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13831 Z= 0.177 Angle : 0.676 14.528 18868 Z= 0.326 Chirality : 0.043 0.280 2239 Planarity : 0.004 0.042 2322 Dihedral : 6.853 78.934 2124 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.65 % Allowed : 27.90 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1732 helix: 2.27 (0.17), residues: 966 sheet: -0.22 (0.46), residues: 125 loop : -1.28 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 143 HIS 0.004 0.001 HIS B 788 PHE 0.020 0.001 PHE B 280 TYR 0.009 0.001 TYR B 292 ARG 0.008 0.000 ARG B1032 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 4) link_NAG-ASN : angle 1.98236 ( 12) link_BETA1-4 : bond 0.00472 ( 5) link_BETA1-4 : angle 1.96126 ( 15) hydrogen bonds : bond 0.04548 ( 769) hydrogen bonds : angle 4.00529 ( 2226) SS BOND : bond 0.00688 ( 6) SS BOND : angle 1.91265 ( 12) covalent geometry : bond 0.00405 (13816) covalent geometry : angle 0.67078 (18829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4150.44 seconds wall clock time: 72 minutes 39.31 seconds (4359.31 seconds total)