Starting phenix.real_space_refine on Wed Mar 4 12:42:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7air_11803/03_2026/7air_11803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7air_11803/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7air_11803/03_2026/7air_11803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7air_11803/03_2026/7air_11803.map" model { file = "/net/cci-nas-00/data/ceres_data/7air_11803/03_2026/7air_11803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7air_11803/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.68, per 1000 atoms: 0.20 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: 1.18 Conformation dependent library (CDL) restraints added in 517.5 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: 0.30 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: 2.36 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4231 1.35 - 1.47: 3518 1.47 - 1.60: 5903 1.60 - 1.72: 12 1.72 - 1.85: 152 Bond restraints: 13816 Sorted by residual: bond pdb=" C4 ATP A1201 " pdb=" C5 ATP A1201 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP B1102 " pdb=" C5 ATP B1102 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C5 ATP A1201 " pdb=" C6 ATP A1201 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.80e+01 bond pdb=" O1B ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 1.477 1.610 -0.133 2.20e-02 2.07e+03 3.66e+01 bond pdb=" O1B ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 1.477 1.608 -0.131 2.20e-02 2.07e+03 3.52e+01 ... (remaining 13811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 18364 2.61 - 5.23: 383 5.23 - 7.84: 64 7.84 - 10.46: 14 10.46 - 13.07: 4 Bond angle restraints: 18829 Sorted by residual: angle pdb=" PA ATP B1102 " pdb=" O3A ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 136.83 123.96 12.87 1.00e+00 1.00e+00 1.66e+02 angle pdb=" PA ATP A1201 " pdb=" O3A ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 136.83 125.68 11.15 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C5 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N3 ATP A1201 " ideal model delta sigma weight residual 126.80 118.27 8.53 1.00e+00 1.00e+00 7.28e+01 angle pdb=" C5 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N3 ATP B1102 " ideal model delta sigma weight residual 126.80 118.82 7.98 1.00e+00 1.00e+00 6.38e+01 angle pdb=" N3 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N9 ATP A1201 " ideal model delta sigma weight residual 127.04 135.13 -8.09 1.15e+00 7.59e-01 4.96e+01 ... (remaining 18824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 7419 21.80 - 43.61: 691 43.61 - 65.41: 115 65.41 - 87.22: 22 87.22 - 109.02: 13 Dihedral angle restraints: 8260 sinusoidal: 3235 harmonic: 5025 Sorted by residual: dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 142.37 -49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual 93.00 136.22 -43.22 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.69 109.02 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1615 0.053 - 0.105: 512 0.105 - 0.158: 103 0.158 - 0.211: 7 0.211 - 0.263: 2 Chirality restraints: 2239 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.30 -0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 2236 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LEU A 137 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 137 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 138 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1026 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASN A1026 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN A1026 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A1027 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 121 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LEU A 121 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 121 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 122 " -0.013 2.00e-02 2.50e+03 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2709 2.76 - 3.30: 13078 3.30 - 3.83: 21217 3.83 - 4.37: 22595 4.37 - 4.90: 41575 Nonbonded interactions: 101174 Sorted by model distance: nonbonded pdb=" OG1 THR A 120 " pdb=" OG SER A 450 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A 430 " pdb=" OH TYR A 466 " model vdw 2.235 3.040 nonbonded pdb=" O PRO B 605 " pdb=" NH2 ARG B 608 " model vdw 2.251 3.120 nonbonded pdb=" O SER B 780 " pdb=" OG SER B 780 " model vdw 2.260 3.040 nonbonded pdb=" O GLY A 479 " pdb=" NH2 ARG A 483 " model vdw 2.262 3.120 ... (remaining 101169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 116 through 233 or resid 244 through 444 or (resid 445 and \ (name N or name CA or name C or name O or name CB )) or resid 446 through 611 o \ r (resid 612 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 13 through 733 or resid 735 through 926 or resid 1014 through 1015 or (resid 101 \ 6 through 1017 and (name N or name CA or name C or name O or name CB )) or resid \ 1018 through 1081)) selection = (chain 'B' and (resid 116 through 733 or resid 735 through 881 or resid 887 thro \ ugh 899 or (resid 900 through 901 and (name N or name CA or name C or name O or \ name CB )) or resid 902 through 914 or (resid 915 through 926 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1014 through 1081)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.133 13831 Z= 0.408 Angle : 0.980 13.073 18868 Z= 0.532 Chirality : 0.051 0.263 2239 Planarity : 0.005 0.045 2322 Dihedral : 17.147 109.020 5020 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.41 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 covalent geometry : bond 0.00848 (13816) covalent geometry : angle 0.96761 (18829) SS BOND : bond 0.00723 ( 6) SS BOND : angle 3.97140 ( 12) hydrogen bonds : bond 0.16054 ( 769) hydrogen bonds : angle 5.51862 ( 2226) link_BETA1-4 : bond 0.00417 ( 5) link_BETA1-4 : angle 3.86845 ( 15) link_NAG-ASN : bond 0.00461 ( 4) link_NAG-ASN : angle 2.64074 ( 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 : 0.495 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: 0.1104 time to fit residues: 53.7136 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 : 0.456 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3919 r_free = 0.3919 target = 0.114181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086928 restraints weight = 40688.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.090357 restraints weight = 18432.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.091882 restraints weight = 9900.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.092129 restraints weight = 8899.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.092263 restraints weight = 7907.257| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13831 Z= 0.167 Angle : 0.715 9.918 18868 Z= 0.351 Chirality : 0.044 0.322 2239 Planarity : 0.004 0.053 2322 Dihedral : 10.036 85.212 2134 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.93 % Allowed : 23.32 % Favored : 72.75 % 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: 1.48 (0.17), residues: 974 sheet: -1.39 (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 0.015 0.001 TYR B 411 PHE 0.017 0.002 PHE B 280 TRP 0.015 0.001 TRP A 849 HIS 0.006 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00374 (13816) covalent geometry : angle 0.70413 (18829) SS BOND : bond 0.01255 ( 6) SS BOND : angle 1.90388 ( 12) hydrogen bonds : bond 0.05700 ( 769) hydrogen bonds : angle 4.40387 ( 2226) link_BETA1-4 : bond 0.00759 ( 5) link_BETA1-4 : angle 3.65820 ( 15) link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 2.53279 ( 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 249 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 542 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8733 (pp) REVERT: A 563 LEU cc_start: 0.8494 (mp) cc_final: 0.8031 (tt) REVERT: A 593 ASN cc_start: 0.9079 (m-40) cc_final: 0.8646 (t0) REVERT: A 623 MET cc_start: 0.8857 (ttp) cc_final: 0.8609 (ttm) REVERT: A 643 LEU cc_start: 0.8807 (tt) cc_final: 0.8591 (mm) REVERT: A 704 LEU cc_start: 0.9188 (mt) cc_final: 0.8612 (tt) REVERT: A 876 MET cc_start: 0.8015 (ttt) cc_final: 0.7707 (tmm) REVERT: B 165 LEU cc_start: 0.8338 (tp) cc_final: 0.8041 (tt) REVERT: B 251 MET cc_start: 0.8807 (ttm) cc_final: 0.8406 (tpp) REVERT: B 630 MET cc_start: 0.8771 (ttp) cc_final: 0.8476 (ttt) outliers start: 55 outliers final: 27 residues processed: 233 average time/residue: 0.0871 time to fit residues: 31.9152 Evaluate side-chains 185 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 412 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: 9.9990 chunk 131 optimal weight: 7.9990 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: 0.5980 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.114633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.087385 restraints weight = 41162.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.090671 restraints weight = 18860.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.091832 restraints weight = 10353.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.092138 restraints weight = 9530.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.092413 restraints weight = 8506.494| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13831 Z= 0.137 Angle : 0.648 9.951 18868 Z= 0.314 Chirality : 0.043 0.341 2239 Planarity : 0.004 0.049 2322 Dihedral : 8.246 71.541 2128 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.43 % Allowed : 24.11 % Favored : 71.46 % 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: 0.46 (0.21), residues: 1732 helix: 1.85 (0.17), residues: 981 sheet: -0.95 (0.44), residues: 134 loop : -2.04 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 903 TYR 0.011 0.001 TYR B 356 PHE 0.018 0.001 PHE B 280 TRP 0.010 0.001 TRP B 501 HIS 0.005 0.001 HIS B 845 Details of bonding type rmsd covalent geometry : bond 0.00304 (13816) covalent geometry : angle 0.63700 (18829) SS BOND : bond 0.00453 ( 6) SS BOND : angle 2.00885 ( 12) hydrogen bonds : bond 0.04818 ( 769) hydrogen bonds : angle 4.12572 ( 2226) link_BETA1-4 : bond 0.00695 ( 5) link_BETA1-4 : angle 3.26800 ( 15) link_NAG-ASN : bond 0.00207 ( 4) link_NAG-ASN : angle 2.26738 ( 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 237 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8719 (tpp) cc_final: 0.8483 (tpp) REVERT: A 542 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8712 (pp) REVERT: A 576 MET cc_start: 0.7682 (mtp) cc_final: 0.7469 (mtp) REVERT: A 633 SER cc_start: 0.9054 (m) cc_final: 0.8840 (p) REVERT: A 643 LEU cc_start: 0.8830 (tt) cc_final: 0.8576 (mm) REVERT: A 704 LEU cc_start: 0.9161 (mt) cc_final: 0.8571 (tt) REVERT: A 809 LYS cc_start: 0.8854 (pttt) cc_final: 0.8624 (pttt) REVERT: B 118 MET cc_start: 0.6622 (ttt) cc_final: 0.6406 (mmp) REVERT: B 122 MET cc_start: 0.7189 (ttm) cc_final: 0.6187 (tmm) REVERT: B 623 MET cc_start: 0.8702 (ttp) cc_final: 0.8489 (ttp) REVERT: B 1063 LEU cc_start: 0.9762 (tp) cc_final: 0.9547 (mp) outliers start: 62 outliers final: 39 residues processed: 220 average time/residue: 0.0887 time to fit residues: 30.9981 Evaluate side-chains 195 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain A residue 263 THR 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 758 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 263 THR 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 524 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 854 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 615 HIS A 837 ASN A 868 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.110478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084162 restraints weight = 39392.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087194 restraints weight = 18282.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.089224 restraints weight = 11385.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.090561 restraints weight = 8390.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091348 restraints weight = 6867.817| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3045 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= 0.164 Angle : 0.648 10.224 18868 Z= 0.313 Chirality : 0.043 0.291 2239 Planarity : 0.004 0.040 2322 Dihedral : 7.557 73.786 2126 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.65 % Allowed : 25.46 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.21), residues: 1732 helix: 2.02 (0.17), residues: 986 sheet: -0.98 (0.43), residues: 136 loop : -1.87 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.012 0.001 TYR B 466 PHE 0.018 0.001 PHE A 541 TRP 0.011 0.001 TRP B 690 HIS 0.004 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00370 (13816) covalent geometry : angle 0.63796 (18829) SS BOND : bond 0.00498 ( 6) SS BOND : angle 2.06502 ( 12) hydrogen bonds : bond 0.04716 ( 769) hydrogen bonds : angle 4.07838 ( 2226) link_BETA1-4 : bond 0.00667 ( 5) link_BETA1-4 : angle 3.06218 ( 15) link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 2.16200 ( 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 225 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8737 (pp) REVERT: A 633 SER cc_start: 0.9033 (m) cc_final: 0.8788 (p) REVERT: A 643 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8571 (mm) REVERT: A 704 LEU cc_start: 0.9163 (mt) cc_final: 0.8534 (tt) REVERT: B 122 MET cc_start: 0.7222 (ttm) cc_final: 0.6152 (tmm) REVERT: B 251 MET cc_start: 0.8826 (ttm) cc_final: 0.8578 (ttm) REVERT: B 583 MET cc_start: 0.8027 (tpp) cc_final: 0.7718 (tpp) REVERT: B 623 MET cc_start: 0.8793 (ttp) cc_final: 0.8491 (ttp) outliers start: 65 outliers final: 47 residues processed: 205 average time/residue: 0.0828 time to fit residues: 27.2318 Evaluate side-chains 201 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 262 MET 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 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 643 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 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 827 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 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 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 624 SER Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 854 ASP Chi-restraints excluded: chain B residue 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: 0.9980 chunk 173 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.111127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.084112 restraints weight = 41914.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.086283 restraints weight = 17709.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087556 restraints weight = 10875.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087973 restraints weight = 9883.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.088040 restraints weight = 8898.932| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13831 Z= 0.228 Angle : 0.690 10.281 18868 Z= 0.338 Chirality : 0.044 0.286 2239 Planarity : 0.004 0.036 2322 Dihedral : 7.509 78.489 2126 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.08 % Allowed : 24.39 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.21), residues: 1732 helix: 2.03 (0.17), residues: 984 sheet: -0.91 (0.45), residues: 124 loop : -1.70 (0.23), residues: 624 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 0.018 0.002 PHE A 541 TRP 0.012 0.001 TRP A 143 HIS 0.005 0.001 HIS A 788 Details of bonding type rmsd covalent geometry : bond 0.00515 (13816) covalent geometry : angle 0.68232 (18829) SS BOND : bond 0.00632 ( 6) SS BOND : angle 1.98318 ( 12) hydrogen bonds : bond 0.05008 ( 769) hydrogen bonds : angle 4.19277 ( 2226) link_BETA1-4 : bond 0.00631 ( 5) link_BETA1-4 : angle 2.78533 ( 15) link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 2.01466 ( 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 236 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 151 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8758 (pp) REVERT: A 593 ASN cc_start: 0.9104 (m-40) cc_final: 0.8792 (t0) REVERT: A 633 SER cc_start: 0.9124 (m) cc_final: 0.8865 (p) REVERT: A 643 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8584 (mm) REVERT: A 808 TRP cc_start: 0.8679 (p-90) cc_final: 0.8255 (p-90) REVERT: A 891 MET cc_start: 0.9128 (mmm) cc_final: 0.8546 (mmm) REVERT: B 122 MET cc_start: 0.7292 (ttm) cc_final: 0.6185 (tmm) REVERT: B 251 MET cc_start: 0.8838 (ttm) cc_final: 0.8462 (tpp) REVERT: B 623 MET cc_start: 0.8808 (ttp) cc_final: 0.8462 (ttp) REVERT: B 813 ASP cc_start: 0.9146 (m-30) cc_final: 0.8873 (t0) REVERT: B 1032 ARG cc_start: 0.8927 (tpm170) cc_final: 0.8663 (tpm170) REVERT: B 1063 LEU cc_start: 0.9779 (tp) cc_final: 0.9545 (mp) outliers start: 85 outliers final: 61 residues processed: 212 average time/residue: 0.0854 time to fit residues: 28.9923 Evaluate side-chains 211 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 ILE 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 643 LEU 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 827 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 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 266 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 391 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 471 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ASP 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 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 857 MET Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN B 131 ASN B 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.114247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.086547 restraints weight = 41246.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.089752 restraints weight = 18625.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.091451 restraints weight = 10468.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091703 restraints weight = 9268.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091733 restraints weight = 8365.105| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13831 Z= 0.114 Angle : 0.612 10.135 18868 Z= 0.293 Chirality : 0.041 0.282 2239 Planarity : 0.003 0.038 2322 Dihedral : 7.166 77.694 2126 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.01 % Allowed : 26.39 % 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: 1.11 (0.21), residues: 1732 helix: 2.25 (0.17), residues: 976 sheet: -0.66 (0.47), residues: 124 loop : -1.49 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 903 TYR 0.009 0.001 TYR B 356 PHE 0.021 0.001 PHE B 280 TRP 0.011 0.001 TRP B 501 HIS 0.003 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00242 (13816) covalent geometry : angle 0.60539 (18829) SS BOND : bond 0.00334 ( 6) SS BOND : angle 1.45759 ( 12) hydrogen bonds : bond 0.04371 ( 769) hydrogen bonds : angle 3.96178 ( 2226) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 2.49564 ( 15) link_NAG-ASN : bond 0.00232 ( 4) link_NAG-ASN : angle 1.98318 ( 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 222 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8692 (pp) REVERT: A 583 MET cc_start: 0.8802 (tpp) cc_final: 0.8590 (tpp) REVERT: A 593 ASN cc_start: 0.9064 (m-40) cc_final: 0.8785 (t0) REVERT: A 623 MET cc_start: 0.9194 (tmm) cc_final: 0.8910 (tmm) REVERT: A 643 LEU cc_start: 0.8797 (tt) cc_final: 0.8555 (mm) REVERT: A 704 LEU cc_start: 0.9090 (mt) cc_final: 0.8830 (pp) REVERT: A 891 MET cc_start: 0.9115 (mmm) cc_final: 0.8902 (tpp) REVERT: B 122 MET cc_start: 0.7356 (ttm) cc_final: 0.6224 (tmm) REVERT: B 251 MET cc_start: 0.8828 (ttm) cc_final: 0.8325 (tpp) REVERT: B 623 MET cc_start: 0.8811 (ttp) cc_final: 0.8320 (ttp) REVERT: B 813 ASP cc_start: 0.9126 (m-30) cc_final: 0.8641 (m-30) REVERT: B 1032 ARG cc_start: 0.8873 (tpm170) cc_final: 0.8610 (tpm170) REVERT: B 1063 LEU cc_start: 0.9777 (tp) cc_final: 0.9549 (mp) outliers start: 56 outliers final: 39 residues processed: 206 average time/residue: 0.0909 time to fit residues: 29.3741 Evaluate side-chains 195 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 563 LEU Chi-restraints excluded: chain A residue 632 VAL 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 827 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 154 LEU 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 424 VAL Chi-restraints excluded: chain B residue 464 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.0070 chunk 61 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 379 ASN B 837 ASN B 868 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.115077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.087767 restraints weight = 41017.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091055 restraints weight = 18902.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092868 restraints weight = 10500.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.092992 restraints weight = 9346.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093223 restraints weight = 8230.499| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13831 Z= 0.112 Angle : 0.603 10.081 18868 Z= 0.288 Chirality : 0.041 0.277 2239 Planarity : 0.003 0.038 2322 Dihedral : 6.908 76.310 2124 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.86 % Allowed : 26.61 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.28 (0.17), residues: 970 sheet: -0.45 (0.47), residues: 123 loop : -1.33 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 806 TYR 0.009 0.001 TYR B 356 PHE 0.013 0.001 PHE B 541 TRP 0.010 0.001 TRP A 143 HIS 0.003 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00237 (13816) covalent geometry : angle 0.59634 (18829) SS BOND : bond 0.00540 ( 6) SS BOND : angle 1.47159 ( 12) hydrogen bonds : bond 0.04162 ( 769) hydrogen bonds : angle 3.89754 ( 2226) link_BETA1-4 : bond 0.00508 ( 5) link_BETA1-4 : angle 2.29875 ( 15) link_NAG-ASN : bond 0.00253 ( 4) link_NAG-ASN : angle 2.09627 ( 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 225 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9142 (mt) REVERT: A 542 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8664 (pp) REVERT: A 593 ASN cc_start: 0.9042 (m-40) cc_final: 0.8793 (t0) REVERT: A 623 MET cc_start: 0.9174 (tmm) cc_final: 0.8728 (tmm) REVERT: A 643 LEU cc_start: 0.8779 (tt) cc_final: 0.8531 (mm) REVERT: A 704 LEU cc_start: 0.9089 (mt) cc_final: 0.8859 (pp) REVERT: A 808 TRP cc_start: 0.8541 (p-90) cc_final: 0.8101 (p-90) REVERT: B 122 MET cc_start: 0.7460 (ttm) cc_final: 0.6361 (tmm) REVERT: B 251 MET cc_start: 0.8793 (ttm) cc_final: 0.8375 (tpp) REVERT: B 309 MET cc_start: 0.8057 (mmm) cc_final: 0.7749 (mmm) REVERT: B 623 MET cc_start: 0.8838 (ttp) cc_final: 0.8588 (ttp) REVERT: B 813 ASP cc_start: 0.9127 (m-30) cc_final: 0.8635 (m-30) REVERT: B 876 MET cc_start: 0.8411 (ttp) cc_final: 0.7917 (ttp) REVERT: B 1032 ARG cc_start: 0.8901 (tpm170) cc_final: 0.8624 (tpm170) REVERT: B 1063 LEU cc_start: 0.9769 (tp) cc_final: 0.9540 (mp) outliers start: 54 outliers final: 38 residues processed: 211 average time/residue: 0.0865 time to fit residues: 29.0416 Evaluate side-chains 202 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 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 624 SER Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 861 LEU 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: 1.9990 chunk 165 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.111292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.085238 restraints weight = 38864.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.088311 restraints weight = 18020.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.090350 restraints weight = 11158.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.091670 restraints weight = 8202.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092522 restraints weight = 6704.303| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13831 Z= 0.135 Angle : 0.623 10.123 18868 Z= 0.301 Chirality : 0.042 0.278 2239 Planarity : 0.004 0.038 2322 Dihedral : 6.867 76.934 2124 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.72 % Allowed : 26.61 % 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: 1.26 (0.21), residues: 1732 helix: 2.28 (0.17), residues: 969 sheet: -0.37 (0.47), residues: 124 loop : -1.26 (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 B 356 PHE 0.019 0.001 PHE B 280 TRP 0.009 0.001 TRP A 143 HIS 0.003 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00306 (13816) covalent geometry : angle 0.61698 (18829) SS BOND : bond 0.00550 ( 6) SS BOND : angle 1.84094 ( 12) hydrogen bonds : bond 0.04288 ( 769) hydrogen bonds : angle 3.92356 ( 2226) link_BETA1-4 : bond 0.00521 ( 5) link_BETA1-4 : angle 2.17565 ( 15) link_NAG-ASN : bond 0.00211 ( 4) link_NAG-ASN : angle 2.09683 ( 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 215 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 643 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 704 LEU cc_start: 0.9096 (mt) cc_final: 0.8836 (pp) REVERT: A 808 TRP cc_start: 0.8476 (p-90) cc_final: 0.8064 (p-90) REVERT: B 122 MET cc_start: 0.7511 (ttm) cc_final: 0.6392 (tmm) REVERT: B 251 MET cc_start: 0.8769 (ttm) cc_final: 0.8369 (tpp) REVERT: B 623 MET cc_start: 0.8901 (ttp) cc_final: 0.8622 (ttp) REVERT: B 813 ASP cc_start: 0.9092 (m-30) cc_final: 0.8612 (m-30) REVERT: B 876 MET cc_start: 0.8261 (ttp) cc_final: 0.7820 (ttp) REVERT: B 1063 LEU cc_start: 0.9752 (tp) cc_final: 0.9552 (mp) outliers start: 52 outliers final: 42 residues processed: 200 average time/residue: 0.0850 time to fit residues: 27.3926 Evaluate side-chains 201 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 279 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 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 827 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 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 643 LEU Chi-restraints excluded: chain B residue 791 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 599 GLN ** 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 = 0.3954 r_free = 0.3954 target = 0.111808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085707 restraints weight = 39542.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.088828 restraints weight = 18211.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090898 restraints weight = 11218.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.092262 restraints weight = 8199.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.093148 restraints weight = 6658.912| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13831 Z= 0.132 Angle : 0.631 10.207 18868 Z= 0.303 Chirality : 0.041 0.278 2239 Planarity : 0.004 0.041 2322 Dihedral : 6.779 77.463 2124 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.79 % Allowed : 27.04 % Favored : 69.17 % 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: 1.27 (0.21), residues: 1732 helix: 2.28 (0.17), residues: 963 sheet: -0.25 (0.47), residues: 123 loop : -1.23 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1032 TYR 0.008 0.001 TYR B 356 PHE 0.013 0.001 PHE A 541 TRP 0.010 0.001 TRP B 607 HIS 0.006 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00296 (13816) covalent geometry : angle 0.62541 (18829) SS BOND : bond 0.00626 ( 6) SS BOND : angle 1.82181 ( 12) hydrogen bonds : bond 0.04263 ( 769) hydrogen bonds : angle 3.93914 ( 2226) link_BETA1-4 : bond 0.00497 ( 5) link_BETA1-4 : angle 2.07625 ( 15) link_NAG-ASN : bond 0.00183 ( 4) link_NAG-ASN : angle 2.07867 ( 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 212 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8696 (pp) REVERT: A 593 ASN cc_start: 0.8960 (t0) cc_final: 0.8398 (t0) REVERT: A 623 MET cc_start: 0.9206 (tmm) cc_final: 0.8461 (tmm) REVERT: A 642 MET cc_start: 0.8686 (tpp) cc_final: 0.8406 (tpp) REVERT: A 643 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8564 (mm) REVERT: A 704 LEU cc_start: 0.9083 (mt) cc_final: 0.8818 (pp) REVERT: A 808 TRP cc_start: 0.8450 (p-90) cc_final: 0.8065 (p-90) REVERT: B 122 MET cc_start: 0.7596 (ttm) cc_final: 0.6523 (tmm) REVERT: B 251 MET cc_start: 0.8775 (ttm) cc_final: 0.8306 (tpp) REVERT: B 297 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8042 (mptt) REVERT: B 623 MET cc_start: 0.8918 (ttp) cc_final: 0.8648 (ttp) REVERT: B 813 ASP cc_start: 0.9087 (m-30) cc_final: 0.8604 (m-30) REVERT: B 875 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7730 (ttp-110) REVERT: B 876 MET cc_start: 0.8270 (ttp) cc_final: 0.7834 (ttp) REVERT: B 1043 MET cc_start: 0.8978 (mtm) cc_final: 0.8765 (pmm) REVERT: B 1063 LEU cc_start: 0.9752 (tp) cc_final: 0.9547 (mp) outliers start: 53 outliers final: 45 residues processed: 196 average time/residue: 0.0823 time to fit residues: 26.1924 Evaluate side-chains 205 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 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 563 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 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 827 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 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 643 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 875 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 30 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 80 optimal weight: 40.0000 chunk 46 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1026 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 = 0.3937 r_free = 0.3937 target = 0.110698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084563 restraints weight = 39377.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.087644 restraints weight = 18306.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089677 restraints weight = 11302.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.091031 restraints weight = 8256.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.091903 restraints weight = 6733.019| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13831 Z= 0.151 Angle : 0.649 10.271 18868 Z= 0.312 Chirality : 0.042 0.277 2239 Planarity : 0.004 0.039 2322 Dihedral : 6.787 78.495 2124 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.65 % Allowed : 27.61 % 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: 1.25 (0.21), residues: 1732 helix: 2.25 (0.17), residues: 965 sheet: -0.29 (0.47), residues: 123 loop : -1.23 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1032 TYR 0.010 0.001 TYR B 466 PHE 0.025 0.001 PHE B 280 TRP 0.009 0.001 TRP A 143 HIS 0.006 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00343 (13816) covalent geometry : angle 0.64329 (18829) SS BOND : bond 0.00644 ( 6) SS BOND : angle 1.85179 ( 12) hydrogen bonds : bond 0.04393 ( 769) hydrogen bonds : angle 3.96988 ( 2226) link_BETA1-4 : bond 0.00454 ( 5) link_BETA1-4 : angle 1.98680 ( 15) link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 2.08901 ( 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 208 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8716 (pp) REVERT: A 593 ASN cc_start: 0.8943 (t0) cc_final: 0.8431 (t0) REVERT: A 704 LEU cc_start: 0.9085 (mt) cc_final: 0.8810 (pp) REVERT: A 806 ARG cc_start: 0.8802 (tpp80) cc_final: 0.8587 (tpp80) REVERT: A 808 TRP cc_start: 0.8456 (p-90) cc_final: 0.8077 (p-90) REVERT: B 122 MET cc_start: 0.7701 (ttm) cc_final: 0.6578 (tmm) REVERT: B 251 MET cc_start: 0.8763 (ttm) cc_final: 0.8321 (tpp) REVERT: B 297 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8047 (mptt) REVERT: B 309 MET cc_start: 0.8048 (mmm) cc_final: 0.7645 (mmm) REVERT: B 389 ASP cc_start: 0.8091 (t70) cc_final: 0.7876 (t70) REVERT: B 623 MET cc_start: 0.8939 (ttp) cc_final: 0.8653 (ttp) REVERT: B 813 ASP cc_start: 0.9086 (m-30) cc_final: 0.8608 (m-30) REVERT: B 876 MET cc_start: 0.8279 (ttp) cc_final: 0.7870 (ttp) REVERT: B 1043 MET cc_start: 0.9008 (mtm) cc_final: 0.8728 (pmm) REVERT: B 1063 LEU cc_start: 0.9761 (tp) cc_final: 0.9555 (mp) outliers start: 51 outliers final: 46 residues processed: 194 average time/residue: 0.0810 time to fit residues: 25.4124 Evaluate side-chains 205 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 266 VAL 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 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 563 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 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 827 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 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 643 LEU 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: 2.9990 chunk 31 optimal weight: 0.0470 chunk 82 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.109813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.082830 restraints weight = 39603.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.085953 restraints weight = 18498.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.088052 restraints weight = 11547.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.089416 restraints weight = 8517.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090305 restraints weight = 6981.662| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13831 Z= 0.152 Angle : 0.644 10.103 18868 Z= 0.310 Chirality : 0.042 0.276 2239 Planarity : 0.004 0.042 2322 Dihedral : 6.776 79.071 2124 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.01 % Allowed : 27.68 % 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: 1.24 (0.21), residues: 1732 helix: 2.24 (0.17), residues: 965 sheet: -0.30 (0.47), residues: 123 loop : -1.21 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1032 TYR 0.009 0.001 TYR B 466 PHE 0.022 0.001 PHE B 280 TRP 0.009 0.001 TRP A 143 HIS 0.005 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00345 (13816) covalent geometry : angle 0.63896 (18829) SS BOND : bond 0.00644 ( 6) SS BOND : angle 1.83061 ( 12) hydrogen bonds : bond 0.04429 ( 769) hydrogen bonds : angle 3.96781 ( 2226) link_BETA1-4 : bond 0.00455 ( 5) link_BETA1-4 : angle 1.94894 ( 15) link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 2.06338 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.97 seconds wall clock time: 37 minutes 45.85 seconds (2265.85 seconds total)