Starting phenix.real_space_refine on Fri Jul 3 10:36:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_11803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_11803.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_11803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_11803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_11803.map" model { file = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_11803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7air_11803/07_2026/7air_11803.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'GLU:plan': 3, 'ASN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 3, 'HIS:plan': 2, 'ASP:plan': 1, 'ARG:plan': 5} 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: {'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 2} 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 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 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 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: 1 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: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.20, per 1000 atoms: 0.16 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: 0.86 Conformation dependent library (CDL) restraints added in 464.9 milliseconds 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: 0.35 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: 1.59 Time building geometry restraints manager: 1.12 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 - 17.91: 7029 17.91 - 35.82: 770 35.82 - 53.73: 186 53.73 - 71.64: 22 71.64 - 89.55: 12 Dihedral angle restraints: 8019 sinusoidal: 2994 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=" CA GLN B 693 " pdb=" C GLN B 693 " pdb=" N LEU B 694 " pdb=" CA LEU B 694 " ideal model delta harmonic sigma weight residual -180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 8016 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: 1.830 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.690 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 15.600 89.545 4779 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.41 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (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 ARG 0.004 0.001 ARG A 710 TYR 0.035 0.002 TYR A 356 PHE 0.024 0.002 PHE A 611 TRP 0.018 0.002 TRP B 381 HIS 0.011 0.002 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.41 (13816) covalent geometry : angle 0.96761 / 0.53 (18829) SS BOND : bond 0.00723 / 0.46 ( 6) SS BOND : angle 3.97140 / 1.87 ( 12) hydrogen bonds : bond 0.16054 / 10.62 ( 769) hydrogen bonds : angle 5.51862 / 3.89 ( 2226) link_BETA1-4 : bond 0.00417 / 0.22 ( 5) link_BETA1-4 : angle 3.86845 / 2.20 ( 15) link_NAG-ASN : bond 0.00461 / 0.33 ( 4) link_NAG-ASN : angle 2.64074 / 1.53 ( 12) *********************** 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 : 0.326 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: 0.7787 (tp) REVERT: A 879 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.5771 (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: 0.0960 time to fit residues: 46.8185 Evaluate side-chains 165 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 344 HIS A 655 GLN A 717 GLN A 732 GLN A 747 GLN A 751 ASN A 853 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.114108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086946 restraints weight = 40709.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090119 restraints weight = 18185.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.092026 restraints weight = 10154.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.092037 restraints weight = 9014.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.092243 restraints weight = 7949.920| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13831 Z= 0.172 Angle : 0.712 9.831 18868 Z= 0.351 Chirality : 0.044 0.334 2239 Planarity : 0.004 0.054 2322 Dihedral : 4.948 59.745 1893 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.93 % Allowed : 23.39 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1732 helix: 1.49 (0.17), residues: 974 sheet: -1.43 (0.43), residues: 134 loop : -2.34 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 903 TYR 0.014 0.001 TYR B 411 PHE 0.017 0.002 PHE A 714 TRP 0.017 0.001 TRP A 849 HIS 0.006 0.001 HIS A 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13816) covalent geometry : angle 0.70250 / 0.35 (18829) SS BOND : bond 0.00512 / 0.27 ( 6) SS BOND : angle 1.89028 / 0.86 ( 12) hydrogen bonds : bond 0.05749 / 3.88 ( 769) hydrogen bonds : angle 4.40639 / 3.10 ( 2226) link_BETA1-4 : bond 0.00647 / 0.34 ( 5) link_BETA1-4 : angle 3.13293 / 1.73 ( 15) link_NAG-ASN : bond 0.00281 / 0.14 ( 4) link_NAG-ASN : angle 2.49374 / 1.47 ( 12) *********************** 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 247 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 0.337 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: A 392 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: A 542 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8729 (pp) REVERT: A 593 ASN cc_start: 0.9079 (m-40) cc_final: 0.8646 (t0) REVERT: A 623 MET cc_start: 0.8865 (ttp) cc_final: 0.8633 (ttm) REVERT: A 643 LEU cc_start: 0.8807 (tt) cc_final: 0.8577 (mm) REVERT: A 704 LEU cc_start: 0.9191 (mt) cc_final: 0.8615 (tt) REVERT: A 876 MET cc_start: 0.8018 (ttt) cc_final: 0.7708 (tmm) REVERT: A 1057 MET cc_start: 0.9593 (tpp) cc_final: 0.9392 (tpt) REVERT: B 165 LEU cc_start: 0.8349 (tp) cc_final: 0.8038 (tt) REVERT: B 484 ASP cc_start: 0.8611 (m-30) cc_final: 0.8283 (t0) REVERT: B 551 ASN cc_start: 0.8917 (t0) cc_final: 0.8679 (m110) REVERT: B 630 MET cc_start: 0.8773 (ttp) cc_final: 0.8478 (ttt) outliers start: 55 outliers final: 27 residues processed: 230 average time/residue: 0.0794 time to fit residues: 28.7583 Evaluate side-chains 184 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 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 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 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 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 424 VAL 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 569 ILE 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 105 optimal weight: 8.9990 chunk 131 optimal weight: 0.3980 chunk 151 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3938 r_free = 0.3938 target = 0.115361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.087845 restraints weight = 41012.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.091352 restraints weight = 19396.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.093286 restraints weight = 10365.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093568 restraints weight = 8828.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.093761 restraints weight = 8071.365| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13831 Z= 0.129 Angle : 0.637 10.077 18868 Z= 0.309 Chirality : 0.042 0.283 2239 Planarity : 0.004 0.053 2322 Dihedral : 4.378 48.338 1887 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.65 % Allowed : 24.68 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1732 helix: 1.86 (0.17), residues: 979 sheet: -0.94 (0.44), residues: 134 loop : -2.04 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 903 TYR 0.010 0.001 TYR B 411 PHE 0.018 0.001 PHE B 280 TRP 0.010 0.001 TRP B 501 HIS 0.004 0.001 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (13816) covalent geometry : angle 0.62828 / 0.31 (18829) SS BOND : bond 0.00356 / 0.19 ( 6) SS BOND : angle 2.12319 / 1.13 ( 12) hydrogen bonds : bond 0.04840 / 3.28 ( 769) hydrogen bonds : angle 4.13134 / 2.90 ( 2226) link_BETA1-4 : bond 0.00783 / 0.43 ( 5) link_BETA1-4 : angle 2.73526 / 1.53 ( 15) link_NAG-ASN : bond 0.00102 / 0.06 ( 4) link_NAG-ASN : angle 2.29744 / 1.24 ( 12) *********************** 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 233 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.522 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: 0.8978 (OUTLIER) cc_final: 0.8709 (pp) REVERT: A 563 LEU cc_start: 0.8404 (mp) cc_final: 0.7944 (tt) REVERT: A 633 SER cc_start: 0.9071 (m) cc_final: 0.8855 (p) REVERT: A 643 LEU cc_start: 0.8800 (tt) cc_final: 0.8558 (mm) REVERT: A 704 LEU cc_start: 0.9145 (mt) cc_final: 0.8561 (tt) REVERT: B 118 MET cc_start: 0.6694 (ttt) cc_final: 0.6361 (mmp) REVERT: B 122 MET cc_start: 0.7185 (ttm) cc_final: 0.6118 (tmm) REVERT: B 251 MET cc_start: 0.8804 (ttm) cc_final: 0.8567 (ttm) REVERT: B 484 ASP cc_start: 0.8423 (m-30) cc_final: 0.8138 (t0) REVERT: B 623 MET cc_start: 0.8688 (ttp) cc_final: 0.8484 (ttp) REVERT: B 1043 MET cc_start: 0.9415 (ptp) cc_final: 0.9123 (ptp) REVERT: B 1063 LEU cc_start: 0.9765 (tp) cc_final: 0.9543 (mp) outliers start: 51 outliers final: 31 residues processed: 220 average time/residue: 0.0803 time to fit residues: 28.3563 Evaluate side-chains 194 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 221 ILE 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 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 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 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 154 LEU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 590 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 615 HIS A 868 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.110134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.083644 restraints weight = 39535.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.086671 restraints weight = 18431.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.088689 restraints weight = 11463.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.090047 restraints weight = 8442.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090922 restraints weight = 6905.485| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2910 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= 0.193 Angle : 0.671 10.026 18868 Z= 0.327 Chirality : 0.043 0.285 2239 Planarity : 0.004 0.041 2322 Dihedral : 4.191 34.668 1885 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.43 % Allowed : 25.46 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1732 helix: 2.00 (0.17), residues: 982 sheet: -0.98 (0.43), residues: 134 loop : -1.89 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.012 0.001 TYR B 292 PHE 0.019 0.002 PHE A 541 TRP 0.010 0.001 TRP A 143 HIS 0.004 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (13816) covalent geometry : angle 0.66283 / 0.32 (18829) SS BOND : bond 0.00561 / 0.34 ( 6) SS BOND : angle 2.12830 / 1.09 ( 12) hydrogen bonds : bond 0.04903 / 3.30 ( 769) hydrogen bonds : angle 4.13150 / 2.89 ( 2226) link_BETA1-4 : bond 0.00593 / 0.33 ( 5) link_BETA1-4 : angle 2.56079 / 1.42 ( 15) link_NAG-ASN : bond 0.00346 / 0.17 ( 4) link_NAG-ASN : angle 2.23479 / 1.17 ( 12) *********************** 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 220 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 158 time to evaluate : 0.499 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 251 MET cc_start: 0.8710 (tpp) cc_final: 0.8510 (tpp) REVERT: A 542 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8767 (pp) REVERT: A 583 MET cc_start: 0.8896 (tpp) cc_final: 0.8658 (tpp) REVERT: A 593 ASN cc_start: 0.9077 (m-40) cc_final: 0.8809 (t0) REVERT: A 643 LEU cc_start: 0.8844 (tt) cc_final: 0.8582 (mm) REVERT: A 704 LEU cc_start: 0.9167 (mt) cc_final: 0.8529 (tt) REVERT: B 484 ASP cc_start: 0.8398 (m-30) cc_final: 0.8049 (t0) REVERT: B 623 MET cc_start: 0.8763 (ttp) cc_final: 0.8480 (ttp) REVERT: B 630 MET cc_start: 0.8627 (tpp) cc_final: 0.8421 (ttm) outliers start: 62 outliers final: 50 residues processed: 200 average time/residue: 0.0746 time to fit residues: 24.1485 Evaluate side-chains 198 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 177 ASN Chi-restraints excluded: chain A residue 221 ILE 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 286 ILE Chi-restraints excluded: chain A residue 320 PHE 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 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 678 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 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU 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 375 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 529 LEU 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 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 861 LEU Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 56 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 599 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.111938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.084982 restraints weight = 41776.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087142 restraints weight = 17533.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.088453 restraints weight = 10827.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.088870 restraints weight = 9748.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.088876 restraints weight = 8805.257| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13831 Z= 0.206 Angle : 0.672 10.151 18868 Z= 0.330 Chirality : 0.043 0.289 2239 Planarity : 0.004 0.036 2322 Dihedral : 4.200 29.292 1885 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.72 % Allowed : 24.82 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1732 helix: 2.07 (0.17), residues: 970 sheet: -1.03 (0.45), residues: 122 loop : -1.75 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 903 TYR 0.012 0.001 TYR B 292 PHE 0.017 0.002 PHE A 541 TRP 0.012 0.001 TRP A 143 HIS 0.004 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (13816) covalent geometry : angle 0.66556 / 0.33 (18829) SS BOND : bond 0.00576 / 0.35 ( 6) SS BOND : angle 1.93883 / 0.98 ( 12) hydrogen bonds : bond 0.04952 / 3.33 ( 769) hydrogen bonds : angle 4.16841 / 2.93 ( 2226) link_BETA1-4 : bond 0.00576 / 0.31 ( 5) link_BETA1-4 : angle 2.39170 / 1.35 ( 15) link_NAG-ASN : bond 0.00199 / 0.11 ( 4) link_NAG-ASN : angle 2.20408 / 1.16 ( 12) *********************** 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 233 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 0.489 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: 0.9073 (OUTLIER) cc_final: 0.8762 (pp) REVERT: A 583 MET cc_start: 0.8879 (tpp) cc_final: 0.8660 (tpp) REVERT: A 593 ASN cc_start: 0.9096 (m-40) cc_final: 0.8763 (t0) REVERT: A 891 MET cc_start: 0.9114 (mmm) cc_final: 0.8514 (mmm) REVERT: B 118 MET cc_start: 0.6502 (ttt) cc_final: 0.6264 (mmp) REVERT: B 122 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.5913 (tmm) REVERT: B 251 MET cc_start: 0.8750 (ttm) cc_final: 0.8536 (ttm) REVERT: B 484 ASP cc_start: 0.8283 (m-30) cc_final: 0.7725 (t0) REVERT: B 623 MET cc_start: 0.8778 (ttp) cc_final: 0.8365 (ttp) REVERT: B 813 ASP cc_start: 0.9147 (m-30) cc_final: 0.8886 (t0) REVERT: B 1032 ARG cc_start: 0.8872 (tpm170) cc_final: 0.8651 (tpm170) REVERT: B 1063 LEU cc_start: 0.9780 (tp) cc_final: 0.9560 (mp) outliers start: 80 outliers final: 54 residues processed: 214 average time/residue: 0.0817 time to fit residues: 27.8615 Evaluate side-chains 204 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 221 ILE 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 289 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 343 CYS 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 678 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 122 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU 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 375 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 424 VAL 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 567 LEU Chi-restraints excluded: chain B residue 570 LEU 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 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 861 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 156 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 379 ASN B 837 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.114951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088016 restraints weight = 41177.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091271 restraints weight = 18056.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.092766 restraints weight = 10081.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.092996 restraints weight = 9043.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093108 restraints weight = 8162.995| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13831 Z= 0.117 Angle : 0.610 9.901 18868 Z= 0.294 Chirality : 0.041 0.289 2239 Planarity : 0.004 0.041 2322 Dihedral : 4.049 29.478 1885 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.15 % Allowed : 27.04 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.21), residues: 1732 helix: 2.28 (0.17), residues: 969 sheet: -0.85 (0.45), residues: 124 loop : -1.55 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 806 TYR 0.008 0.001 TYR B 636 PHE 0.020 0.001 PHE B 280 TRP 0.012 0.001 TRP B 808 HIS 0.003 0.001 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (13816) covalent geometry : angle 0.60382 / 0.29 (18829) SS BOND : bond 0.00326 / 0.19 ( 6) SS BOND : angle 1.49216 / 0.77 ( 12) hydrogen bonds : bond 0.04292 / 2.91 ( 769) hydrogen bonds : angle 3.90682 / 2.73 ( 2226) link_BETA1-4 : bond 0.00583 / 0.31 ( 5) link_BETA1-4 : angle 2.24021 / 1.24 ( 15) link_NAG-ASN : bond 0.00300 / 0.17 ( 4) link_NAG-ASN : angle 2.12749 / 1.13 ( 12) *********************** 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 208 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 583 MET cc_start: 0.8769 (tpp) cc_final: 0.8548 (tpp) REVERT: A 593 ASN cc_start: 0.9057 (m-40) cc_final: 0.8800 (t0) REVERT: A 623 MET cc_start: 0.9201 (tmm) cc_final: 0.8977 (tmm) REVERT: A 643 LEU cc_start: 0.8781 (tt) cc_final: 0.8553 (mm) REVERT: A 704 LEU cc_start: 0.9082 (mt) cc_final: 0.8824 (pp) REVERT: A 891 MET cc_start: 0.9090 (mmm) cc_final: 0.8498 (mmm) REVERT: B 122 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.5814 (tmm) REVERT: B 251 MET cc_start: 0.8742 (ttm) cc_final: 0.8231 (tpp) REVERT: B 484 ASP cc_start: 0.8172 (m-30) cc_final: 0.7684 (t0) REVERT: B 488 ASP cc_start: 0.7777 (m-30) cc_final: 0.7009 (t0) REVERT: B 623 MET cc_start: 0.8719 (ttp) cc_final: 0.8453 (ttp) REVERT: B 813 ASP cc_start: 0.9128 (m-30) cc_final: 0.8635 (m-30) REVERT: B 1032 ARG cc_start: 0.8869 (tpm170) cc_final: 0.8619 (tpm170) REVERT: B 1063 LEU cc_start: 0.9775 (tp) cc_final: 0.9541 (mp) outliers start: 44 outliers final: 30 residues processed: 195 average time/residue: 0.0784 time to fit residues: 24.2264 Evaluate side-chains 190 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 279 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR 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 604 THR 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 122 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.0670 chunk 61 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 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 = 0.3945 r_free = 0.3945 target = 0.116062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.087638 restraints weight = 41039.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.091025 restraints weight = 20400.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.093158 restraints weight = 11100.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.093511 restraints weight = 9050.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.093677 restraints weight = 8502.628| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13831 Z= 0.113 Angle : 0.614 9.923 18868 Z= 0.293 Chirality : 0.041 0.286 2239 Planarity : 0.004 0.038 2322 Dihedral : 3.857 26.649 1883 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.22 % Allowed : 27.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1732 helix: 2.24 (0.17), residues: 975 sheet: -0.52 (0.46), residues: 123 loop : -1.40 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 806 TYR 0.007 0.001 TYR B 636 PHE 0.012 0.001 PHE A 714 TRP 0.011 0.001 TRP B 808 HIS 0.003 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13816) covalent geometry : angle 0.60810 / 0.29 (18829) SS BOND : bond 0.00969 / 0.56 ( 6) SS BOND : angle 1.72763 / 0.94 ( 12) hydrogen bonds : bond 0.04094 / 2.79 ( 769) hydrogen bonds : angle 3.86918 / 2.71 ( 2226) link_BETA1-4 : bond 0.00537 / 0.31 ( 5) link_BETA1-4 : angle 2.12540 / 1.18 ( 15) link_NAG-ASN : bond 0.00257 / 0.15 ( 4) link_NAG-ASN : angle 2.12994 / 1.13 ( 12) *********************** 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 215 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9137 (mt) REVERT: A 542 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8667 (pp) REVERT: A 583 MET cc_start: 0.8710 (tpp) cc_final: 0.8486 (tpp) REVERT: A 643 LEU cc_start: 0.8752 (tt) cc_final: 0.8523 (mm) REVERT: A 704 LEU cc_start: 0.9096 (mt) cc_final: 0.8843 (pp) REVERT: A 891 MET cc_start: 0.9087 (mmm) cc_final: 0.8505 (mmm) REVERT: A 1068 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7810 (pt0) REVERT: B 122 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.5843 (tmm) REVERT: B 251 MET cc_start: 0.8760 (ttm) cc_final: 0.8305 (tpp) REVERT: B 484 ASP cc_start: 0.8145 (m-30) cc_final: 0.7590 (t0) REVERT: B 488 ASP cc_start: 0.7735 (m-30) cc_final: 0.6995 (t0) REVERT: B 583 MET cc_start: 0.7572 (mmp) cc_final: 0.7327 (tpp) REVERT: B 623 MET cc_start: 0.8831 (ttp) cc_final: 0.8567 (ttp) REVERT: B 792 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8610 (m) REVERT: B 813 ASP cc_start: 0.9121 (m-30) cc_final: 0.8637 (m-30) REVERT: B 1032 ARG cc_start: 0.8823 (tpm170) cc_final: 0.8574 (tpm170) REVERT: B 1063 LEU cc_start: 0.9771 (tp) cc_final: 0.9541 (mp) outliers start: 45 outliers final: 27 residues processed: 203 average time/residue: 0.0776 time to fit residues: 25.5117 Evaluate side-chains 191 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 279 LEU 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 426 ILE Chi-restraints excluded: chain A residue 495 VAL 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 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 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 624 SER Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 792 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3936 r_free = 0.3936 target = 0.115434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.086581 restraints weight = 40897.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.090093 restraints weight = 21545.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.091452 restraints weight = 11468.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092213 restraints weight = 10290.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.092466 restraints weight = 9283.524| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13831 Z= 0.126 Angle : 0.616 9.966 18868 Z= 0.296 Chirality : 0.041 0.287 2239 Planarity : 0.003 0.041 2322 Dihedral : 3.857 26.046 1883 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.43 % Allowed : 26.90 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1732 helix: 2.29 (0.17), residues: 969 sheet: -0.43 (0.46), residues: 124 loop : -1.34 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 806 TYR 0.008 0.001 TYR A 649 PHE 0.020 0.001 PHE B 280 TRP 0.017 0.001 TRP B 690 HIS 0.002 0.001 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13816) covalent geometry : angle 0.60949 / 0.29 (18829) SS BOND : bond 0.00619 / 0.35 ( 6) SS BOND : angle 1.86475 / 0.97 ( 12) hydrogen bonds : bond 0.04149 / 2.81 ( 769) hydrogen bonds : angle 3.85726 / 2.68 ( 2226) link_BETA1-4 : bond 0.00537 / 0.30 ( 5) link_BETA1-4 : angle 2.04621 / 1.15 ( 15) link_NAG-ASN : bond 0.00216 / 0.13 ( 4) link_NAG-ASN : angle 2.09885 / 1.11 ( 12) *********************** 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: 48 poor density : 165 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 LEU cc_start: 0.8683 (mt) cc_final: 0.8454 (tt) REVERT: A 542 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8677 (pp) REVERT: A 583 MET cc_start: 0.8736 (tpp) cc_final: 0.8503 (tpp) REVERT: A 593 ASN cc_start: 0.8921 (t0) cc_final: 0.8322 (t0) REVERT: A 623 MET cc_start: 0.9169 (tmm) cc_final: 0.8430 (tmm) REVERT: A 643 LEU cc_start: 0.8756 (tt) cc_final: 0.8549 (mm) REVERT: A 704 LEU cc_start: 0.9098 (mt) cc_final: 0.8843 (pp) REVERT: A 808 TRP cc_start: 0.8535 (p-90) cc_final: 0.8099 (p-90) REVERT: A 891 MET cc_start: 0.9091 (mmm) cc_final: 0.8551 (mmm) REVERT: A 1068 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: B 122 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.5851 (tmm) REVERT: B 251 MET cc_start: 0.8786 (ttm) cc_final: 0.8360 (tpp) REVERT: B 297 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8035 (mptt) REVERT: B 389 ASP cc_start: 0.8019 (t70) cc_final: 0.7805 (t70) REVERT: B 488 ASP cc_start: 0.7799 (m-30) cc_final: 0.6389 (t0) REVERT: B 623 MET cc_start: 0.8855 (ttp) cc_final: 0.8579 (ttp) REVERT: B 792 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8657 (m) REVERT: B 813 ASP cc_start: 0.9149 (m-30) cc_final: 0.8661 (m-30) REVERT: B 857 MET cc_start: 0.9158 (mmt) cc_final: 0.8919 (mmp) REVERT: B 876 MET cc_start: 0.8438 (ttp) cc_final: 0.7961 (ttp) REVERT: B 1063 LEU cc_start: 0.9776 (tp) cc_final: 0.9534 (mp) outliers start: 48 outliers final: 35 residues processed: 200 average time/residue: 0.0754 time to fit residues: 24.0128 Evaluate side-chains 196 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 258 PHE 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 415 ASP 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 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 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 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 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 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 624 SER Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 792 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 32 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085696 restraints weight = 41836.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.088910 restraints weight = 21214.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.090949 restraints weight = 11646.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090976 restraints weight = 9658.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.091344 restraints weight = 9326.224| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13831 Z= 0.158 Angle : 0.639 10.122 18868 Z= 0.310 Chirality : 0.042 0.283 2239 Planarity : 0.004 0.050 2322 Dihedral : 3.878 26.788 1883 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.72 % Allowed : 27.04 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1732 helix: 2.25 (0.17), residues: 971 sheet: -0.40 (0.46), residues: 123 loop : -1.27 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1032 TYR 0.008 0.001 TYR B 292 PHE 0.015 0.001 PHE A 541 TRP 0.014 0.001 TRP B 690 HIS 0.003 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (13816) covalent geometry : angle 0.63381 / 0.31 (18829) SS BOND : bond 0.00654 / 0.37 ( 6) SS BOND : angle 1.89325 / 0.97 ( 12) hydrogen bonds : bond 0.04411 / 2.97 ( 769) hydrogen bonds : angle 3.90062 / 2.71 ( 2226) link_BETA1-4 : bond 0.00494 / 0.27 ( 5) link_BETA1-4 : angle 1.98522 / 1.13 ( 15) link_NAG-ASN : bond 0.00159 / 0.10 ( 4) link_NAG-ASN : angle 1.91013 / 1.01 ( 12) *********************** 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 209 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.8697 (mmm) cc_final: 0.8495 (tpt) REVERT: A 309 MET cc_start: 0.8757 (mmp) cc_final: 0.8399 (mmm) REVERT: A 464 LEU cc_start: 0.8711 (mt) cc_final: 0.8476 (tt) REVERT: A 542 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8688 (pp) REVERT: A 583 MET cc_start: 0.8777 (tpp) cc_final: 0.8561 (tpp) REVERT: A 593 ASN cc_start: 0.8968 (t0) cc_final: 0.8441 (t0) REVERT: A 623 MET cc_start: 0.9169 (tmm) cc_final: 0.8425 (tmm) REVERT: A 643 LEU cc_start: 0.8757 (tt) cc_final: 0.8537 (mm) REVERT: A 704 LEU cc_start: 0.9098 (mt) cc_final: 0.8865 (pp) REVERT: A 808 TRP cc_start: 0.8562 (p-90) cc_final: 0.8131 (p-90) REVERT: A 1068 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: B 122 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.5916 (tmm) REVERT: B 251 MET cc_start: 0.8787 (ttm) cc_final: 0.8388 (tpp) REVERT: B 297 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8059 (mptt) REVERT: B 488 ASP cc_start: 0.7905 (m-30) cc_final: 0.6501 (t0) REVERT: B 623 MET cc_start: 0.8850 (ttp) cc_final: 0.8590 (ttp) REVERT: B 813 ASP cc_start: 0.9156 (m-30) cc_final: 0.8671 (m-30) REVERT: B 875 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7641 (ttp-110) REVERT: B 876 MET cc_start: 0.8444 (ttp) cc_final: 0.7937 (ttp) outliers start: 52 outliers final: 40 residues processed: 195 average time/residue: 0.0789 time to fit residues: 24.5574 Evaluate side-chains 199 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 258 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 279 LEU 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 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 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 A residue 1068 GLU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 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 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 750 LYS 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 30 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 133 optimal weight: 0.4980 chunk 80 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN ** 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 = 0.3942 r_free = 0.3942 target = 0.115920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.088185 restraints weight = 41483.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090709 restraints weight = 17673.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.092807 restraints weight = 10759.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.093016 restraints weight = 9661.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093098 restraints weight = 8216.391| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13831 Z= 0.115 Angle : 0.631 10.055 18868 Z= 0.301 Chirality : 0.041 0.288 2239 Planarity : 0.004 0.040 2322 Dihedral : 3.848 25.147 1883 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.72 % Allowed : 28.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1732 helix: 2.26 (0.17), residues: 970 sheet: -0.24 (0.47), residues: 123 loop : -1.26 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1032 TYR 0.007 0.001 TYR A 649 PHE 0.022 0.001 PHE B 280 TRP 0.015 0.001 TRP B 690 HIS 0.007 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (13816) covalent geometry : angle 0.62568 / 0.30 (18829) SS BOND : bond 0.00521 / 0.29 ( 6) SS BOND : angle 1.67384 / 0.85 ( 12) hydrogen bonds : bond 0.04162 / 2.82 ( 769) hydrogen bonds : angle 3.83909 / 2.67 ( 2226) link_BETA1-4 : bond 0.00535 / 0.29 ( 5) link_BETA1-4 : angle 1.92329 / 1.08 ( 15) link_NAG-ASN : bond 0.00215 / 0.12 ( 4) link_NAG-ASN : angle 1.94384 / 1.02 ( 12) ********************** 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 200 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8189 (ttm) cc_final: 0.7597 (tmm) REVERT: A 309 MET cc_start: 0.8730 (mmp) cc_final: 0.8374 (mmm) REVERT: A 464 LEU cc_start: 0.8672 (mt) cc_final: 0.8455 (tt) REVERT: A 542 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8673 (pp) REVERT: A 593 ASN cc_start: 0.8918 (t0) cc_final: 0.8406 (t0) REVERT: A 643 LEU cc_start: 0.8729 (tt) cc_final: 0.8507 (mm) REVERT: A 704 LEU cc_start: 0.9111 (mt) cc_final: 0.8854 (pp) REVERT: A 808 TRP cc_start: 0.8517 (p-90) cc_final: 0.8158 (p-90) REVERT: A 1068 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: B 122 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.5896 (tmm) REVERT: B 251 MET cc_start: 0.8785 (ttm) cc_final: 0.8326 (tpp) REVERT: B 488 ASP cc_start: 0.7801 (m-30) cc_final: 0.6369 (t0) REVERT: B 583 MET cc_start: 0.7589 (mmp) cc_final: 0.7340 (tpp) REVERT: B 623 MET cc_start: 0.8856 (ttp) cc_final: 0.8585 (ttp) REVERT: B 813 ASP cc_start: 0.9136 (m-30) cc_final: 0.8644 (m-30) REVERT: B 876 MET cc_start: 0.8461 (ttp) cc_final: 0.7974 (ttp) REVERT: B 1063 LEU cc_start: 0.9781 (tp) cc_final: 0.9522 (mp) outliers start: 38 outliers final: 32 residues processed: 192 average time/residue: 0.0734 time to fit residues: 23.1992 Evaluate side-chains 193 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 258 PHE Chi-restraints excluded: chain A residue 263 THR 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 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 604 THR Chi-restraints excluded: chain A residue 631 PHE 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 1060 LEU Chi-restraints excluded: chain A residue 1068 GLU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 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 624 SER Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 138 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.115911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.088544 restraints weight = 41393.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.090998 restraints weight = 17717.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093503 restraints weight = 10645.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.093683 restraints weight = 9145.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.093721 restraints weight = 7723.711| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13831 Z= 0.116 Angle : 0.620 10.281 18868 Z= 0.297 Chirality : 0.041 0.286 2239 Planarity : 0.004 0.039 2322 Dihedral : 3.826 24.707 1883 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.79 % Allowed : 28.90 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1732 helix: 2.19 (0.17), residues: 979 sheet: -0.12 (0.47), residues: 123 loop : -1.26 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1032 TYR 0.010 0.001 TYR A 649 PHE 0.021 0.001 PHE B 280 TRP 0.015 0.001 TRP B 690 HIS 0.006 0.001 HIS A 776 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (13816) covalent geometry : angle 0.61550 / 0.30 (18829) SS BOND : bond 0.00488 / 0.27 ( 6) SS BOND : angle 1.62820 / 0.82 ( 12) hydrogen bonds : bond 0.04017 / 2.72 ( 769) hydrogen bonds : angle 3.84467 / 2.68 ( 2226) link_BETA1-4 : bond 0.00607 / 0.33 ( 5) link_BETA1-4 : angle 1.84573 / 1.06 ( 15) link_NAG-ASN : bond 0.00206 / 0.12 ( 4) link_NAG-ASN : angle 1.96824 / 1.04 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.49 seconds wall clock time: 32 minutes 58.40 seconds (1978.40 seconds total)