Starting phenix.real_space_refine on Thu Jul 31 20:33:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aiq_11802/07_2025/7aiq_11802.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aiq_11802/07_2025/7aiq_11802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2025/7aiq_11802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2025/7aiq_11802.map" model { file = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2025/7aiq_11802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aiq_11802/07_2025/7aiq_11802.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.039 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 4 5.49 5 S 96 5.16 5 C 8769 2.51 5 N 2223 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 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13514 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6695 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6659 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 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: "A" 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 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.49, per 1000 atoms: 0.63 Number of scatterers: 13514 At special positions: 0 Unit cell: (107.1, 111.35, 151.3, 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 4 15.00 O 2422 8.00 N 2223 7.00 C 8769 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=2.04 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-ASN " NAG A1101 " - " ASN A 361 " " NAG B1101 " - " ASN B 361 " " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN B 312 " Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 1.8 seconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 120 through 133 removed outlier: 6.010A 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 135 through 141 Processing helix chain 'A' and resid 141 through 177 removed outlier: 6.496A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 removed outlier: 4.234A pdb=" N MET A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.518A pdb=" N LEU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.956A 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: 5.445A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.146A 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: 3.878A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.743A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) 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 440 through 444 removed outlier: 3.605A pdb=" N LEU A 444 " --> pdb=" O SER A 441 " (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: 4.035A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 3.654A 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: 3.899A pdb=" N LEU A 542 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 543 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.824A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 4.195A 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: 4.127A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.746A pdb=" N THR A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.544A 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: 3.623A pdb=" N LYS A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.527A 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 887 through 903 removed outlier: 4.000A pdb=" N MET A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 932 removed outlier: 3.861A pdb=" N GLU A 924 " --> pdb=" O ALA A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1033 removed outlier: 3.604A pdb=" N ARG A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 3.632A pdb=" N THR A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 133 removed outlier: 5.912A 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 Processing helix chain 'B' and resid 141 through 177 removed outlier: 6.623A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.603A pdb=" N LEU B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.825A 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: 5.652A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.113A 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: 3.937A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.985A 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 420 through 428 Processing helix chain 'B' and resid 429 through 432 Processing helix chain 'B' and resid 440 through 444 removed outlier: 3.685A pdb=" N LEU B 444 " --> pdb=" O SER B 441 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 504 through 536 removed outlier: 3.922A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) removed outlier: 3.627A 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 543 through 547 Processing helix chain 'B' and resid 557 through 570 Processing helix chain 'B' and resid 573 through 603 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.630A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 4.023A 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: 4.081A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 3.784A pdb=" N THR B 713 " --> pdb=" O PRO B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.730A pdb=" N ALA B 742 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 756 " --> pdb=" O MET B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 780 removed outlier: 3.622A pdb=" N ALA B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 820 removed outlier: 3.551A pdb=" N LYS B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 813 " --> pdb=" O LYS B 809 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 removed outlier: 3.642A 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 888 through 903 removed outlier: 3.832A pdb=" N HIS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 926 removed outlier: 5.263A pdb=" N ALA B 920 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR B 921 " --> pdb=" O ASP B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1033 removed outlier: 3.504A pdb=" N MET B1019 " --> pdb=" O ASN B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 3.834A 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: 3.793A 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: 3.517A pdb=" N ILE A 726 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 695 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 791 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1072 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N LEU A1040 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP A 847 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASN A1042 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 907 " --> pdb=" O MET A 876 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 880 " --> pdb=" O GLU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.641A 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: 3.650A pdb=" N LEU B 310 " --> pdb=" O ARG B 313 " (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 767 removed outlier: 6.795A pdb=" N THR B 725 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLN B 763 " --> pdb=" O THR B 725 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL B 727 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL B 765 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 729 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA B 767 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE B 731 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 791 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B1072 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N LEU B1040 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP B 847 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN B1042 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 846 " --> pdb=" O ARG B 877 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE B 879 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 848 " --> pdb=" O PHE B 879 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET B 876 " --> pdb=" O GLU B 907 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU B 909 " --> pdb=" O MET B 876 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE B 878 " --> pdb=" O GLU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.578A pdb=" N LEU B 783 " --> pdb=" O MET B 786 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 4.48 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: 4235 1.35 - 1.47: 3479 1.47 - 1.59: 5957 1.59 - 1.72: 8 1.72 - 1.84: 152 Bond restraints: 13831 Sorted by residual: bond pdb=" C4 ATP B1102 " pdb=" C5 ATP B1102 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP A1102 " pdb=" C5 ATP A1102 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C5 ATP B1102 " pdb=" C6 ATP B1102 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.08e+01 bond pdb=" O1B ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 1.477 1.609 -0.132 2.20e-02 2.07e+03 3.58e+01 bond pdb=" O1B ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 1.477 1.607 -0.130 2.20e-02 2.07e+03 3.48e+01 ... (remaining 13826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 18388 2.79 - 5.58: 384 5.58 - 8.36: 51 8.36 - 11.15: 17 11.15 - 13.94: 4 Bond angle restraints: 18844 Sorted by residual: angle pdb=" PA ATP A1102 " pdb=" O3A ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 136.83 122.89 13.94 1.00e+00 1.00e+00 1.94e+02 angle pdb=" PA ATP B1102 " pdb=" O3A ATP B1102 " pdb=" PB ATP B1102 " ideal model delta sigma weight residual 136.83 124.70 12.13 1.00e+00 1.00e+00 1.47e+02 angle pdb=" C5 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N3 ATP B1102 " ideal model delta sigma weight residual 126.80 118.38 8.42 1.00e+00 1.00e+00 7.08e+01 angle pdb=" C5 ATP A1102 " pdb=" C4 ATP A1102 " pdb=" N3 ATP A1102 " ideal model delta sigma weight residual 126.80 118.45 8.35 1.00e+00 1.00e+00 6.97e+01 angle pdb=" N3 ATP B1102 " pdb=" C4 ATP B1102 " pdb=" N9 ATP B1102 " ideal model delta sigma weight residual 127.04 135.12 -8.08 1.15e+00 7.59e-01 4.95e+01 ... (remaining 18839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 7549 24.48 - 48.97: 596 48.97 - 73.45: 63 73.45 - 97.93: 23 97.93 - 122.41: 25 Dihedral angle restraints: 8256 sinusoidal: 3245 harmonic: 5011 Sorted by residual: 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 93.00 138.12 -45.12 1 1.00e+01 1.00e-02 2.83e+01 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 93.00 134.12 -41.12 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C5 NAG C 2 " ideal model delta sinusoidal sigma weight residual -62.96 59.45 -122.41 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 8253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1563 0.051 - 0.103: 541 0.103 - 0.154: 103 0.154 - 0.205: 17 0.205 - 0.257: 5 Chirality restraints: 2229 Sorted by residual: chirality pdb=" CB VAL A 881 " pdb=" CA VAL A 881 " pdb=" CG1 VAL A 881 " pdb=" CG2 VAL A 881 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 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 -2.53 0.25 2.00e-01 2.50e+01 1.60e+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 -2.52 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2226 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU A 137 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 137 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 138 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 121 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C LEU B 121 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 121 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 122 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO B 409 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.028 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1919 2.74 - 3.28: 13369 3.28 - 3.82: 21304 3.82 - 4.36: 23058 4.36 - 4.90: 41742 Nonbonded interactions: 101392 Sorted by model distance: nonbonded pdb=" OG1 THR A 314 " pdb=" O VAL A 391 " model vdw 2.202 3.040 nonbonded pdb=" NE2 GLN A 152 " pdb=" OH TYR A 384 " model vdw 2.227 3.120 nonbonded pdb=" OG SER B 430 " pdb=" OH TYR B 466 " model vdw 2.245 3.040 nonbonded pdb=" O GLY A 479 " pdb=" NH2 ARG A 483 " model vdw 2.245 3.120 nonbonded pdb=" O SER B 780 " pdb=" OG SER B 780 " model vdw 2.254 3.040 ... (remaining 101387 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 881 or resid 887 through 926 or resid 1014 thr \ ough 1081 or resid 1101 through 1102)) selection = (chain 'B' and (resid 116 through 233 or resid 244 through 347 or (resid 348 and \ (name N or name CA or name C or name O or name CB )) or resid 349 through 912 o \ r (resid 913 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 14 through 1019 or (resid 1020 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1021 through 1081 or resid 1101 through 1102)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.320 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.009 0.132 13845 Z= 0.419 Angle : 1.024 13.940 18880 Z= 0.562 Chirality : 0.053 0.257 2229 Planarity : 0.005 0.050 2326 Dihedral : 18.348 122.414 5028 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.20 % Allowed : 20.95 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1731 helix: 0.32 (0.16), residues: 953 sheet: -1.90 (0.41), residues: 136 loop : -2.74 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 795 HIS 0.011 0.002 HIS B 853 PHE 0.026 0.003 PHE B 541 TYR 0.021 0.002 TYR A 356 ARG 0.005 0.001 ARG B 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 4) link_NAG-ASN : angle 2.85943 ( 12) link_BETA1-4 : bond 0.01538 ( 4) link_BETA1-4 : angle 3.56861 ( 12) hydrogen bonds : bond 0.15785 ( 764) hydrogen bonds : angle 5.75474 ( 2211) SS BOND : bond 0.00558 ( 6) SS BOND : angle 3.88512 ( 12) covalent geometry : bond 0.00869 (13831) covalent geometry : angle 1.01383 (18844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 307 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8251 (mtp) cc_final: 0.7775 (tmm) REVERT: A 144 MET cc_start: 0.8485 (ttp) cc_final: 0.8037 (ptm) REVERT: A 186 TYR cc_start: 0.8882 (t80) cc_final: 0.8591 (t80) REVERT: A 188 MET cc_start: 0.7584 (mtm) cc_final: 0.7211 (ttt) REVERT: A 313 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6262 (mtm-85) REVERT: A 358 MET cc_start: 0.9423 (mpp) cc_final: 0.9108 (mpp) REVERT: A 391 VAL cc_start: 0.8254 (t) cc_final: 0.7669 (t) REVERT: A 630 MET cc_start: 0.8819 (ttp) cc_final: 0.8449 (ttp) REVERT: A 658 GLU cc_start: 0.8283 (tt0) cc_final: 0.7922 (mm-30) REVERT: A 752 MET cc_start: 0.9315 (tpp) cc_final: 0.8882 (tpp) REVERT: A 859 MET cc_start: 0.9326 (mtp) cc_final: 0.8793 (mmp) REVERT: A 878 ILE cc_start: 0.8829 (mt) cc_final: 0.8614 (mm) REVERT: A 1074 ARG cc_start: 0.8646 (ttt90) cc_final: 0.8376 (ttt90) REVERT: A 1078 ARG cc_start: 0.8653 (mtm110) cc_final: 0.8316 (ptm160) REVERT: B 118 MET cc_start: 0.8444 (ptm) cc_final: 0.7770 (ptm) REVERT: B 122 MET cc_start: 0.8997 (mtp) cc_final: 0.8205 (tmm) REVERT: B 385 LEU cc_start: 0.9527 (mt) cc_final: 0.9058 (mt) REVERT: B 419 SER cc_start: 0.8544 (t) cc_final: 0.7926 (p) REVERT: B 563 LEU cc_start: 0.8774 (mp) cc_final: 0.8524 (tt) REVERT: B 596 CYS cc_start: 0.8318 (m) cc_final: 0.8034 (t) REVERT: B 630 MET cc_start: 0.9050 (ttp) cc_final: 0.8621 (ttm) REVERT: B 659 LYS cc_start: 0.9087 (tttt) cc_final: 0.8728 (ttmm) REVERT: B 696 VAL cc_start: 0.9062 (t) cc_final: 0.8849 (m) REVERT: B 746 GLU cc_start: 0.8805 (tt0) cc_final: 0.8264 (tp30) REVERT: B 750 LYS cc_start: 0.9389 (mttt) cc_final: 0.8569 (mttp) REVERT: B 752 MET cc_start: 0.8794 (tpp) cc_final: 0.8564 (tpp) REVERT: B 791 VAL cc_start: 0.9485 (t) cc_final: 0.9196 (m) REVERT: B 813 ASP cc_start: 0.9114 (m-30) cc_final: 0.8845 (t0) REVERT: B 857 MET cc_start: 0.8982 (ptm) cc_final: 0.8624 (pmm) REVERT: B 874 CYS cc_start: 0.8415 (m) cc_final: 0.6985 (t) REVERT: B 1055 ASN cc_start: 0.9231 (m110) cc_final: 0.8759 (t0) outliers start: 17 outliers final: 9 residues processed: 321 average time/residue: 0.2474 time to fit residues: 115.8245 Evaluate side-chains 174 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 699 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 344 HIS A 521 GLN A 655 GLN A 732 GLN A 751 ASN B 130 GLN B 152 GLN B 250 ASN B 344 HIS B 655 GLN B 717 GLN B 732 GLN B 747 GLN B 751 ASN B 763 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.095381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.069636 restraints weight = 39414.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.072611 restraints weight = 18851.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.074613 restraints weight = 11681.074| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13845 Z= 0.155 Angle : 0.689 9.014 18880 Z= 0.340 Chirality : 0.043 0.240 2229 Planarity : 0.004 0.050 2326 Dihedral : 13.033 105.622 2121 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.25 % Allowed : 22.36 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1731 helix: 1.46 (0.17), residues: 953 sheet: -1.13 (0.41), residues: 133 loop : -2.36 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.005 0.001 HIS A 845 PHE 0.018 0.002 PHE B 863 TYR 0.016 0.001 TYR A 292 ARG 0.006 0.001 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 4) link_NAG-ASN : angle 1.84366 ( 12) link_BETA1-4 : bond 0.01058 ( 4) link_BETA1-4 : angle 3.59441 ( 12) hydrogen bonds : bond 0.05574 ( 764) hydrogen bonds : angle 4.41874 ( 2211) SS BOND : bond 0.00382 ( 6) SS BOND : angle 1.99686 ( 12) covalent geometry : bond 0.00337 (13831) covalent geometry : angle 0.68054 (18844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8195 (mtp) cc_final: 0.7795 (tmm) REVERT: A 144 MET cc_start: 0.8289 (ttp) cc_final: 0.7955 (ptm) REVERT: A 147 THR cc_start: 0.8492 (t) cc_final: 0.8244 (t) REVERT: A 186 TYR cc_start: 0.8705 (t80) cc_final: 0.8314 (t80) REVERT: A 188 MET cc_start: 0.7578 (mtm) cc_final: 0.7223 (ttt) REVERT: A 358 MET cc_start: 0.9427 (mpp) cc_final: 0.9048 (mpp) REVERT: A 376 LEU cc_start: 0.8864 (tp) cc_final: 0.8635 (tp) REVERT: A 484 ASP cc_start: 0.8366 (m-30) cc_final: 0.7788 (p0) REVERT: A 542 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8323 (pp) REVERT: A 631 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8434 (t80) REVERT: A 658 GLU cc_start: 0.8387 (tt0) cc_final: 0.7984 (mm-30) REVERT: A 752 MET cc_start: 0.9298 (tpp) cc_final: 0.8813 (tpp) REVERT: A 753 MET cc_start: 0.9167 (ttp) cc_final: 0.8633 (ptm) REVERT: A 791 VAL cc_start: 0.9117 (t) cc_final: 0.8809 (p) REVERT: A 848 VAL cc_start: 0.8667 (t) cc_final: 0.8246 (m) REVERT: A 854 ASP cc_start: 0.8378 (m-30) cc_final: 0.8117 (m-30) REVERT: A 859 MET cc_start: 0.9203 (mtp) cc_final: 0.8671 (mmp) REVERT: A 864 LEU cc_start: 0.9360 (mt) cc_final: 0.9153 (mp) REVERT: A 1078 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8229 (ptm160) REVERT: B 353 CYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (m) REVERT: B 380 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8712 (tt) REVERT: B 419 SER cc_start: 0.8465 (t) cc_final: 0.8134 (p) REVERT: B 542 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8294 (pp) REVERT: B 576 MET cc_start: 0.8361 (mtp) cc_final: 0.8044 (mtp) REVERT: B 587 MET cc_start: 0.8977 (tpt) cc_final: 0.8590 (tpt) REVERT: B 623 MET cc_start: 0.9373 (tmm) cc_final: 0.8789 (tmm) REVERT: B 630 MET cc_start: 0.8856 (ttp) cc_final: 0.8570 (ttm) REVERT: B 659 LYS cc_start: 0.9077 (tttt) cc_final: 0.8684 (ttmm) REVERT: B 693 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8177 (mm110) REVERT: B 699 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7917 (tttt) REVERT: B 712 LEU cc_start: 0.8823 (mt) cc_final: 0.8475 (mt) REVERT: B 750 LYS cc_start: 0.9389 (mttt) cc_final: 0.9048 (mtmm) REVERT: B 813 ASP cc_start: 0.9119 (m-30) cc_final: 0.8844 (t0) REVERT: B 874 CYS cc_start: 0.8592 (m) cc_final: 0.7401 (t) REVERT: B 1055 ASN cc_start: 0.9195 (m110) cc_final: 0.8717 (t0) outliers start: 60 outliers final: 29 residues processed: 256 average time/residue: 0.2000 time to fit residues: 81.4597 Evaluate side-chains 205 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 0.0570 chunk 75 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN B 763 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070818 restraints weight = 39573.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.073781 restraints weight = 18943.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075773 restraints weight = 11739.751| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13845 Z= 0.143 Angle : 0.646 11.509 18880 Z= 0.311 Chirality : 0.042 0.218 2229 Planarity : 0.004 0.052 2326 Dihedral : 11.893 102.356 2108 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.60 % Allowed : 23.57 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1731 helix: 1.84 (0.17), residues: 953 sheet: -0.64 (0.43), residues: 133 loop : -2.08 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.005 0.001 HIS B 853 PHE 0.014 0.001 PHE A 620 TYR 0.011 0.001 TYR A 292 ARG 0.005 0.000 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 4) link_NAG-ASN : angle 1.57740 ( 12) link_BETA1-4 : bond 0.00929 ( 4) link_BETA1-4 : angle 3.46737 ( 12) hydrogen bonds : bond 0.04838 ( 764) hydrogen bonds : angle 4.10303 ( 2211) SS BOND : bond 0.00272 ( 6) SS BOND : angle 1.79523 ( 12) covalent geometry : bond 0.00319 (13831) covalent geometry : angle 0.63819 (18844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 174 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8247 (mtp) cc_final: 0.7850 (tmm) REVERT: A 144 MET cc_start: 0.8262 (ttp) cc_final: 0.7979 (ptm) REVERT: A 147 THR cc_start: 0.8595 (t) cc_final: 0.8352 (t) REVERT: A 188 MET cc_start: 0.7526 (mtm) cc_final: 0.7236 (ttm) REVERT: A 358 MET cc_start: 0.9448 (mpp) cc_final: 0.9057 (mpp) REVERT: A 376 LEU cc_start: 0.8889 (tp) cc_final: 0.8677 (tp) REVERT: A 533 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7832 (tp) REVERT: A 536 ASP cc_start: 0.8092 (t70) cc_final: 0.7884 (t0) REVERT: A 658 GLU cc_start: 0.8465 (tt0) cc_final: 0.8009 (mm-30) REVERT: A 752 MET cc_start: 0.9296 (tpp) cc_final: 0.8766 (tpp) REVERT: A 854 ASP cc_start: 0.8269 (m-30) cc_final: 0.8034 (m-30) REVERT: A 859 MET cc_start: 0.9117 (mtp) cc_final: 0.8713 (mmp) REVERT: A 1043 MET cc_start: 0.9262 (ptt) cc_final: 0.8857 (pmm) REVERT: A 1078 ARG cc_start: 0.8600 (mtm110) cc_final: 0.8258 (ptm160) REVERT: B 171 MET cc_start: 0.8953 (tpp) cc_final: 0.8713 (tpp) REVERT: B 380 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8760 (tt) REVERT: B 419 SER cc_start: 0.8514 (t) cc_final: 0.8279 (p) REVERT: B 542 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8292 (pp) REVERT: B 576 MET cc_start: 0.8316 (mtp) cc_final: 0.8018 (mtp) REVERT: B 587 MET cc_start: 0.8865 (tpt) cc_final: 0.8560 (tpt) REVERT: B 623 MET cc_start: 0.9360 (tmm) cc_final: 0.8755 (tmm) REVERT: B 630 MET cc_start: 0.8665 (ttp) cc_final: 0.8389 (ttm) REVERT: B 659 LYS cc_start: 0.9060 (tttt) cc_final: 0.8701 (ttmm) REVERT: B 750 LYS cc_start: 0.9380 (mttt) cc_final: 0.9083 (mtmm) REVERT: B 813 ASP cc_start: 0.9078 (m-30) cc_final: 0.8810 (t0) REVERT: B 874 CYS cc_start: 0.8699 (m) cc_final: 0.7468 (t) REVERT: B 876 MET cc_start: 0.8760 (ttp) cc_final: 0.8475 (ttp) REVERT: B 1055 ASN cc_start: 0.9210 (m110) cc_final: 0.8790 (t0) outliers start: 65 outliers final: 41 residues processed: 226 average time/residue: 0.1899 time to fit residues: 68.3751 Evaluate side-chains 200 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 117 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 0.0020 chunk 141 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN B 615 HIS ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.070113 restraints weight = 39689.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073033 restraints weight = 19017.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075056 restraints weight = 11855.684| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13845 Z= 0.168 Angle : 0.642 10.690 18880 Z= 0.310 Chirality : 0.042 0.222 2229 Planarity : 0.003 0.042 2326 Dihedral : 11.176 98.052 2103 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.10 % Allowed : 23.92 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1731 helix: 1.98 (0.17), residues: 950 sheet: -0.58 (0.44), residues: 121 loop : -1.86 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.006 0.001 HIS B 853 PHE 0.021 0.001 PHE A 541 TYR 0.014 0.001 TYR A 186 ARG 0.004 0.000 ARG A1074 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 4) link_NAG-ASN : angle 1.52379 ( 12) link_BETA1-4 : bond 0.00898 ( 4) link_BETA1-4 : angle 3.36028 ( 12) hydrogen bonds : bond 0.04713 ( 764) hydrogen bonds : angle 4.04419 ( 2211) SS BOND : bond 0.00308 ( 6) SS BOND : angle 1.61650 ( 12) covalent geometry : bond 0.00380 (13831) covalent geometry : angle 0.63443 (18844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 158 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8286 (mtp) cc_final: 0.7836 (tmm) REVERT: A 144 MET cc_start: 0.8270 (ttp) cc_final: 0.7919 (ptm) REVERT: A 147 THR cc_start: 0.8584 (t) cc_final: 0.8350 (t) REVERT: A 186 TYR cc_start: 0.8797 (t80) cc_final: 0.8462 (t80) REVERT: A 188 MET cc_start: 0.7558 (mtm) cc_final: 0.7323 (ttm) REVERT: A 358 MET cc_start: 0.9463 (mpp) cc_final: 0.9218 (mpp) REVERT: A 536 ASP cc_start: 0.8451 (t0) cc_final: 0.8233 (t0) REVERT: A 658 GLU cc_start: 0.8471 (tt0) cc_final: 0.8001 (mm-30) REVERT: A 752 MET cc_start: 0.9306 (tpp) cc_final: 0.8774 (tpp) REVERT: A 791 VAL cc_start: 0.9109 (t) cc_final: 0.8838 (p) REVERT: A 859 MET cc_start: 0.9165 (mtp) cc_final: 0.8719 (mmp) REVERT: A 876 MET cc_start: 0.9018 (ttp) cc_final: 0.8810 (ttp) REVERT: A 1041 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7983 (pt) REVERT: A 1042 ASN cc_start: 0.8221 (p0) cc_final: 0.7797 (p0) REVERT: A 1043 MET cc_start: 0.9296 (ptt) cc_final: 0.8823 (pmm) REVERT: A 1078 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8310 (ptm160) REVERT: B 258 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8366 (t80) REVERT: B 419 SER cc_start: 0.8499 (t) cc_final: 0.8170 (p) REVERT: B 542 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8245 (pp) REVERT: B 576 MET cc_start: 0.8326 (mtp) cc_final: 0.8025 (mtp) REVERT: B 587 MET cc_start: 0.8765 (tpt) cc_final: 0.8535 (tpt) REVERT: B 659 LYS cc_start: 0.9029 (tttt) cc_final: 0.8673 (ttmm) REVERT: B 750 LYS cc_start: 0.9400 (mttt) cc_final: 0.9094 (mtmm) REVERT: B 813 ASP cc_start: 0.9083 (m-30) cc_final: 0.8840 (t0) REVERT: B 874 CYS cc_start: 0.8778 (m) cc_final: 0.7470 (t) REVERT: B 876 MET cc_start: 0.8732 (ttp) cc_final: 0.8469 (ttp) REVERT: B 1055 ASN cc_start: 0.9226 (m110) cc_final: 0.8825 (t0) outliers start: 72 outliers final: 53 residues processed: 219 average time/residue: 0.1936 time to fit residues: 68.5596 Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 HIS B 763 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069474 restraints weight = 40235.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072403 restraints weight = 19148.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.074411 restraints weight = 11915.491| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13845 Z= 0.174 Angle : 0.650 11.839 18880 Z= 0.311 Chirality : 0.042 0.223 2229 Planarity : 0.003 0.035 2326 Dihedral : 10.714 97.308 2101 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.17 % Allowed : 25.19 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1731 helix: 2.06 (0.17), residues: 950 sheet: -0.55 (0.42), residues: 137 loop : -1.69 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 143 HIS 0.005 0.001 HIS A 788 PHE 0.020 0.001 PHE B1059 TYR 0.012 0.001 TYR A 186 ARG 0.003 0.000 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 1.46304 ( 12) link_BETA1-4 : bond 0.00811 ( 4) link_BETA1-4 : angle 3.56059 ( 12) hydrogen bonds : bond 0.04670 ( 764) hydrogen bonds : angle 4.02621 ( 2211) SS BOND : bond 0.00306 ( 6) SS BOND : angle 1.56726 ( 12) covalent geometry : bond 0.00392 (13831) covalent geometry : angle 0.64256 (18844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8309 (mtp) cc_final: 0.7840 (tmm) REVERT: A 144 MET cc_start: 0.8271 (ttp) cc_final: 0.7934 (ptm) REVERT: A 147 THR cc_start: 0.8604 (t) cc_final: 0.8382 (t) REVERT: A 160 CYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 186 TYR cc_start: 0.8818 (t80) cc_final: 0.8471 (t80) REVERT: A 188 MET cc_start: 0.7693 (mtm) cc_final: 0.7398 (ttm) REVERT: A 358 MET cc_start: 0.9495 (mpp) cc_final: 0.9248 (mpp) REVERT: A 658 GLU cc_start: 0.8458 (tt0) cc_final: 0.7975 (mm-30) REVERT: A 752 MET cc_start: 0.9306 (tpp) cc_final: 0.8929 (tpp) REVERT: A 791 VAL cc_start: 0.9121 (t) cc_final: 0.8891 (p) REVERT: A 806 ARG cc_start: 0.8655 (mmt90) cc_final: 0.8139 (tmt170) REVERT: A 859 MET cc_start: 0.9230 (mtp) cc_final: 0.8741 (mmp) REVERT: A 1041 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8004 (pt) REVERT: A 1042 ASN cc_start: 0.8255 (p0) cc_final: 0.7846 (p0) REVERT: A 1043 MET cc_start: 0.9305 (ptt) cc_final: 0.8803 (pmm) REVERT: A 1078 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8376 (ptm160) REVERT: B 171 MET cc_start: 0.9013 (tpp) cc_final: 0.8792 (tpp) REVERT: B 258 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8270 (t80) REVERT: B 416 ILE cc_start: 0.9441 (tt) cc_final: 0.9120 (mm) REVERT: B 419 SER cc_start: 0.8454 (t) cc_final: 0.8109 (p) REVERT: B 542 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8258 (pp) REVERT: B 576 MET cc_start: 0.8315 (mtp) cc_final: 0.7996 (mtp) REVERT: B 587 MET cc_start: 0.8850 (tpt) cc_final: 0.8581 (tpt) REVERT: B 630 MET cc_start: 0.8951 (ttm) cc_final: 0.8585 (ttm) REVERT: B 659 LYS cc_start: 0.9024 (tttt) cc_final: 0.8673 (ttmm) REVERT: B 750 LYS cc_start: 0.9403 (mttt) cc_final: 0.9096 (mtmm) REVERT: B 813 ASP cc_start: 0.9084 (m-30) cc_final: 0.8847 (t0) REVERT: B 874 CYS cc_start: 0.8793 (m) cc_final: 0.7496 (t) REVERT: B 876 MET cc_start: 0.8727 (ttp) cc_final: 0.8478 (ttp) REVERT: B 1055 ASN cc_start: 0.9183 (m110) cc_final: 0.8761 (t0) REVERT: B 1057 MET cc_start: 0.9284 (tpp) cc_final: 0.8996 (tpp) outliers start: 73 outliers final: 60 residues processed: 221 average time/residue: 0.2076 time to fit residues: 72.3676 Evaluate side-chains 217 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072035 restraints weight = 40118.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075046 restraints weight = 18867.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077178 restraints weight = 11588.757| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13845 Z= 0.110 Angle : 0.612 13.961 18880 Z= 0.286 Chirality : 0.041 0.249 2229 Planarity : 0.003 0.037 2326 Dihedral : 9.466 93.088 2101 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.68 % Allowed : 26.82 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1731 helix: 2.19 (0.17), residues: 957 sheet: -0.44 (0.44), residues: 124 loop : -1.54 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 635 HIS 0.004 0.001 HIS B 853 PHE 0.018 0.001 PHE B 261 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 4) link_NAG-ASN : angle 1.36934 ( 12) link_BETA1-4 : bond 0.00212 ( 4) link_BETA1-4 : angle 4.62665 ( 12) hydrogen bonds : bond 0.04043 ( 764) hydrogen bonds : angle 3.86138 ( 2211) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.39454 ( 12) covalent geometry : bond 0.00231 (13831) covalent geometry : angle 0.59933 (18844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 1.491 Fit side-chains REVERT: A 122 MET cc_start: 0.8297 (mtp) cc_final: 0.7831 (tmm) REVERT: A 144 MET cc_start: 0.8204 (ttp) cc_final: 0.7897 (ptm) REVERT: A 147 THR cc_start: 0.8610 (t) cc_final: 0.8379 (t) REVERT: A 160 CYS cc_start: 0.8768 (m) cc_final: 0.8104 (p) REVERT: A 186 TYR cc_start: 0.8757 (t80) cc_final: 0.8445 (t80) REVERT: A 188 MET cc_start: 0.7692 (mtm) cc_final: 0.7403 (ttm) REVERT: A 358 MET cc_start: 0.9487 (mpp) cc_final: 0.9245 (mpp) REVERT: A 576 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.6892 (tpp) REVERT: A 658 GLU cc_start: 0.8406 (tt0) cc_final: 0.8025 (tp30) REVERT: A 752 MET cc_start: 0.9306 (tpp) cc_final: 0.8904 (tpp) REVERT: A 757 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8798 (mmmm) REVERT: A 806 ARG cc_start: 0.8645 (mmt90) cc_final: 0.8133 (mmp80) REVERT: A 859 MET cc_start: 0.9223 (mtp) cc_final: 0.8709 (mmp) REVERT: A 1041 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7942 (pt) REVERT: A 1042 ASN cc_start: 0.8192 (p0) cc_final: 0.7877 (p0) REVERT: A 1043 MET cc_start: 0.9294 (ptt) cc_final: 0.8854 (pmm) REVERT: A 1078 ARG cc_start: 0.8711 (mtm110) cc_final: 0.8373 (ptm160) REVERT: B 171 MET cc_start: 0.8945 (tpp) cc_final: 0.8699 (tpp) REVERT: B 258 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8305 (t80) REVERT: B 390 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8896 (mm) REVERT: B 416 ILE cc_start: 0.9411 (tt) cc_final: 0.9125 (mm) REVERT: B 419 SER cc_start: 0.8252 (t) cc_final: 0.7862 (t) REVERT: B 450 SER cc_start: 0.9424 (t) cc_final: 0.8857 (p) REVERT: B 542 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8174 (pp) REVERT: B 576 MET cc_start: 0.8309 (mtp) cc_final: 0.8003 (mtp) REVERT: B 587 MET cc_start: 0.8793 (tpt) cc_final: 0.8551 (tpt) REVERT: B 630 MET cc_start: 0.8959 (ttm) cc_final: 0.8685 (ttm) REVERT: B 659 LYS cc_start: 0.9003 (tttt) cc_final: 0.8621 (ttmm) REVERT: B 750 LYS cc_start: 0.9369 (mttt) cc_final: 0.9080 (mtmm) REVERT: B 781 CYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8269 (m) REVERT: B 813 ASP cc_start: 0.9040 (m-30) cc_final: 0.8798 (t0) REVERT: B 1055 ASN cc_start: 0.9192 (m110) cc_final: 0.8756 (t0) outliers start: 52 outliers final: 34 residues processed: 223 average time/residue: 0.2126 time to fit residues: 74.2328 Evaluate side-chains 203 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 165 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071905 restraints weight = 40268.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074911 restraints weight = 19066.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077019 restraints weight = 11741.861| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13845 Z= 0.112 Angle : 0.595 11.258 18880 Z= 0.282 Chirality : 0.040 0.219 2229 Planarity : 0.003 0.038 2326 Dihedral : 8.744 89.487 2101 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.54 % Allowed : 27.74 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1731 helix: 2.23 (0.17), residues: 957 sheet: -0.37 (0.46), residues: 117 loop : -1.47 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 143 HIS 0.004 0.001 HIS B 853 PHE 0.022 0.001 PHE B1059 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 4) link_NAG-ASN : angle 1.48713 ( 12) link_BETA1-4 : bond 0.00749 ( 4) link_BETA1-4 : angle 3.44793 ( 12) hydrogen bonds : bond 0.03981 ( 764) hydrogen bonds : angle 3.83025 ( 2211) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.45244 ( 12) covalent geometry : bond 0.00241 (13831) covalent geometry : angle 0.58682 (18844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8237 (mtp) cc_final: 0.7792 (tmm) REVERT: A 144 MET cc_start: 0.8194 (ttp) cc_final: 0.7918 (ptm) REVERT: A 147 THR cc_start: 0.8641 (t) cc_final: 0.8409 (t) REVERT: A 160 CYS cc_start: 0.8757 (m) cc_final: 0.8060 (p) REVERT: A 186 TYR cc_start: 0.8769 (t80) cc_final: 0.8476 (t80) REVERT: A 188 MET cc_start: 0.7655 (mtm) cc_final: 0.7448 (ttm) REVERT: A 309 MET cc_start: 0.8720 (mmm) cc_final: 0.8497 (tpp) REVERT: A 358 MET cc_start: 0.9488 (mpp) cc_final: 0.9248 (mpp) REVERT: A 576 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6291 (tpp) REVERT: A 658 GLU cc_start: 0.8398 (tt0) cc_final: 0.7924 (mm-30) REVERT: A 752 MET cc_start: 0.9314 (tpp) cc_final: 0.8908 (tpp) REVERT: A 859 MET cc_start: 0.9225 (mtp) cc_final: 0.8703 (mmp) REVERT: A 1041 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7931 (pt) REVERT: A 1042 ASN cc_start: 0.8124 (p0) cc_final: 0.7839 (p0) REVERT: A 1043 MET cc_start: 0.9304 (ptt) cc_final: 0.8857 (pmm) REVERT: A 1078 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8369 (ptm160) REVERT: B 171 MET cc_start: 0.8934 (tpp) cc_final: 0.8681 (tpp) REVERT: B 258 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8339 (t80) REVERT: B 416 ILE cc_start: 0.9412 (tt) cc_final: 0.9133 (mm) REVERT: B 450 SER cc_start: 0.9440 (t) cc_final: 0.8885 (p) REVERT: B 542 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8208 (pp) REVERT: B 576 MET cc_start: 0.8310 (mtp) cc_final: 0.8004 (mtp) REVERT: B 587 MET cc_start: 0.8838 (tpt) cc_final: 0.8496 (tpt) REVERT: B 630 MET cc_start: 0.8958 (ttm) cc_final: 0.8747 (ttm) REVERT: B 659 LYS cc_start: 0.9011 (tttt) cc_final: 0.8623 (ttmm) REVERT: B 781 CYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 813 ASP cc_start: 0.9018 (m-30) cc_final: 0.8756 (t0) REVERT: B 1055 ASN cc_start: 0.9205 (m110) cc_final: 0.8774 (t0) outliers start: 50 outliers final: 36 residues processed: 214 average time/residue: 0.2065 time to fit residues: 70.5192 Evaluate side-chains 204 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 380 LEU 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 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 148 optimal weight: 0.0770 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.0010 chunk 130 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 142 optimal weight: 0.0030 chunk 169 optimal weight: 0.0470 chunk 45 optimal weight: 0.7980 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074074 restraints weight = 39658.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.077195 restraints weight = 18756.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079321 restraints weight = 11536.694| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 13845 Z= 0.107 Angle : 0.598 11.794 18880 Z= 0.283 Chirality : 0.040 0.225 2229 Planarity : 0.003 0.040 2326 Dihedral : 8.182 82.080 2101 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.34 % Allowed : 28.52 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1731 helix: 2.23 (0.17), residues: 954 sheet: -0.15 (0.46), residues: 117 loop : -1.35 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 635 HIS 0.005 0.001 HIS B 853 PHE 0.029 0.001 PHE B1059 TYR 0.013 0.001 TYR B1056 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 1.07088 ( 12) link_BETA1-4 : bond 0.00703 ( 4) link_BETA1-4 : angle 3.31946 ( 12) hydrogen bonds : bond 0.03549 ( 764) hydrogen bonds : angle 3.77221 ( 2211) SS BOND : bond 0.00198 ( 6) SS BOND : angle 1.23269 ( 12) covalent geometry : bond 0.00223 (13831) covalent geometry : angle 0.59173 (18844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8210 (mtp) cc_final: 0.7787 (tmm) REVERT: A 144 MET cc_start: 0.8133 (ttp) cc_final: 0.7903 (ptm) REVERT: A 147 THR cc_start: 0.8616 (t) cc_final: 0.8384 (t) REVERT: A 160 CYS cc_start: 0.8720 (m) cc_final: 0.8000 (p) REVERT: A 186 TYR cc_start: 0.8723 (t80) cc_final: 0.8480 (t80) REVERT: A 309 MET cc_start: 0.8738 (mmm) cc_final: 0.8514 (tpp) REVERT: A 358 MET cc_start: 0.9486 (mpp) cc_final: 0.9239 (mpp) REVERT: A 576 MET cc_start: 0.7037 (tpt) cc_final: 0.6524 (tpp) REVERT: A 636 TYR cc_start: 0.7847 (p90) cc_final: 0.7593 (p90) REVERT: A 658 GLU cc_start: 0.8331 (tt0) cc_final: 0.7870 (mm-30) REVERT: A 752 MET cc_start: 0.9303 (tpp) cc_final: 0.8877 (tpp) REVERT: A 781 CYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8285 (t) REVERT: A 859 MET cc_start: 0.9198 (mtp) cc_final: 0.8639 (mmp) REVERT: A 1042 ASN cc_start: 0.8028 (p0) cc_final: 0.7705 (p0) REVERT: A 1043 MET cc_start: 0.9269 (ptt) cc_final: 0.8864 (pmm) REVERT: A 1078 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8325 (ptm160) REVERT: B 171 MET cc_start: 0.8950 (tpp) cc_final: 0.8714 (tpp) REVERT: B 258 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8351 (t80) REVERT: B 416 ILE cc_start: 0.9371 (tt) cc_final: 0.9099 (mm) REVERT: B 450 SER cc_start: 0.9391 (t) cc_final: 0.8847 (p) REVERT: B 521 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 542 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8157 (pp) REVERT: B 576 MET cc_start: 0.8241 (mtp) cc_final: 0.7952 (mtp) REVERT: B 587 MET cc_start: 0.8756 (tpt) cc_final: 0.8453 (tpt) REVERT: B 659 LYS cc_start: 0.8943 (tttt) cc_final: 0.8544 (ttmm) REVERT: B 750 LYS cc_start: 0.9272 (mttt) cc_final: 0.9048 (mttp) REVERT: B 781 CYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7857 (m) REVERT: B 813 ASP cc_start: 0.9002 (m-30) cc_final: 0.8718 (t0) REVERT: B 876 MET cc_start: 0.8643 (ttp) cc_final: 0.8330 (tmm) REVERT: B 1055 ASN cc_start: 0.9186 (m110) cc_final: 0.8739 (t0) outliers start: 33 outliers final: 22 residues processed: 230 average time/residue: 0.2095 time to fit residues: 77.0482 Evaluate side-chains 205 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 118 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 141 optimal weight: 0.0670 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072542 restraints weight = 39984.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075627 restraints weight = 18904.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077693 restraints weight = 11628.035| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13845 Z= 0.117 Angle : 0.627 11.208 18880 Z= 0.292 Chirality : 0.041 0.257 2229 Planarity : 0.003 0.038 2326 Dihedral : 7.825 77.806 2099 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.76 % Allowed : 29.16 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1731 helix: 2.23 (0.17), residues: 957 sheet: -0.29 (0.43), residues: 131 loop : -1.25 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 607 HIS 0.005 0.001 HIS B 853 PHE 0.013 0.001 PHE B 541 TYR 0.019 0.001 TYR A 186 ARG 0.002 0.000 ARG A1074 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 4) link_NAG-ASN : angle 1.05869 ( 12) link_BETA1-4 : bond 0.00673 ( 4) link_BETA1-4 : angle 3.18482 ( 12) hydrogen bonds : bond 0.03783 ( 764) hydrogen bonds : angle 3.78291 ( 2211) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.34142 ( 12) covalent geometry : bond 0.00256 (13831) covalent geometry : angle 0.62076 (18844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8233 (mtp) cc_final: 0.7794 (tmm) REVERT: A 144 MET cc_start: 0.8188 (ttp) cc_final: 0.7924 (ptm) REVERT: A 147 THR cc_start: 0.8643 (t) cc_final: 0.8414 (t) REVERT: A 160 CYS cc_start: 0.8727 (m) cc_final: 0.8027 (p) REVERT: A 186 TYR cc_start: 0.8858 (t80) cc_final: 0.8618 (t80) REVERT: A 289 LEU cc_start: 0.8550 (mt) cc_final: 0.8338 (tt) REVERT: A 313 ARG cc_start: 0.6905 (mtm180) cc_final: 0.6594 (mtm-85) REVERT: A 358 MET cc_start: 0.9491 (mpp) cc_final: 0.9244 (mpp) REVERT: A 576 MET cc_start: 0.7206 (tpt) cc_final: 0.6672 (tpp) REVERT: A 586 LEU cc_start: 0.8459 (mt) cc_final: 0.8208 (tp) REVERT: A 636 TYR cc_start: 0.7877 (p90) cc_final: 0.7625 (p90) REVERT: A 658 GLU cc_start: 0.8315 (tt0) cc_final: 0.7845 (mm-30) REVERT: A 752 MET cc_start: 0.9301 (tpp) cc_final: 0.8871 (tpp) REVERT: A 859 MET cc_start: 0.9233 (mtp) cc_final: 0.8655 (mmp) REVERT: A 1042 ASN cc_start: 0.8020 (p0) cc_final: 0.7656 (p0) REVERT: A 1043 MET cc_start: 0.9304 (ptt) cc_final: 0.8880 (pmm) REVERT: A 1078 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8324 (ptm160) REVERT: B 171 MET cc_start: 0.8960 (tpp) cc_final: 0.8706 (tpp) REVERT: B 258 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8327 (t80) REVERT: B 416 ILE cc_start: 0.9380 (tt) cc_final: 0.9128 (mm) REVERT: B 450 SER cc_start: 0.9447 (t) cc_final: 0.8846 (p) REVERT: B 521 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 542 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8199 (pp) REVERT: B 576 MET cc_start: 0.8256 (mtp) cc_final: 0.7944 (mtp) REVERT: B 587 MET cc_start: 0.8943 (tpt) cc_final: 0.8641 (tpt) REVERT: B 623 MET cc_start: 0.9450 (ppp) cc_final: 0.9202 (tmm) REVERT: B 659 LYS cc_start: 0.8969 (tttt) cc_final: 0.8561 (ttmm) REVERT: B 750 LYS cc_start: 0.9278 (mttt) cc_final: 0.8934 (mttp) REVERT: B 781 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8108 (m) REVERT: B 813 ASP cc_start: 0.9014 (m-30) cc_final: 0.8746 (t0) REVERT: B 876 MET cc_start: 0.8625 (ttp) cc_final: 0.8286 (tmm) REVERT: B 1055 ASN cc_start: 0.9185 (m110) cc_final: 0.8759 (t0) outliers start: 39 outliers final: 29 residues processed: 215 average time/residue: 0.2220 time to fit residues: 75.0040 Evaluate side-chains 209 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 853 HIS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 69 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 763 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.097491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071933 restraints weight = 40148.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074976 restraints weight = 19102.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077065 restraints weight = 11812.307| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13845 Z= 0.130 Angle : 0.646 12.253 18880 Z= 0.301 Chirality : 0.041 0.262 2229 Planarity : 0.003 0.039 2326 Dihedral : 7.631 73.992 2099 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.55 % Allowed : 29.51 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1731 helix: 2.28 (0.17), residues: 952 sheet: -0.35 (0.43), residues: 131 loop : -1.21 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 690 HIS 0.003 0.001 HIS A 788 PHE 0.023 0.001 PHE A 620 TYR 0.013 0.001 TYR B1056 ARG 0.002 0.000 ARG A1074 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 4) link_NAG-ASN : angle 1.03509 ( 12) link_BETA1-4 : bond 0.00831 ( 4) link_BETA1-4 : angle 3.21903 ( 12) hydrogen bonds : bond 0.03889 ( 764) hydrogen bonds : angle 3.78467 ( 2211) SS BOND : bond 0.00283 ( 6) SS BOND : angle 1.43555 ( 12) covalent geometry : bond 0.00296 (13831) covalent geometry : angle 0.63972 (18844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8267 (mtp) cc_final: 0.7811 (tmm) REVERT: A 144 MET cc_start: 0.8205 (ttp) cc_final: 0.7927 (ptm) REVERT: A 147 THR cc_start: 0.8625 (t) cc_final: 0.8400 (t) REVERT: A 160 CYS cc_start: 0.8744 (m) cc_final: 0.8034 (p) REVERT: A 251 MET cc_start: 0.9125 (mmt) cc_final: 0.8787 (mmt) REVERT: A 289 LEU cc_start: 0.8586 (mt) cc_final: 0.8371 (tt) REVERT: A 358 MET cc_start: 0.9495 (mpp) cc_final: 0.9240 (mpp) REVERT: A 576 MET cc_start: 0.7145 (tpt) cc_final: 0.6710 (tpp) REVERT: A 636 TYR cc_start: 0.7874 (p90) cc_final: 0.7634 (p90) REVERT: A 658 GLU cc_start: 0.8323 (tt0) cc_final: 0.7980 (tp30) REVERT: A 752 MET cc_start: 0.9305 (tpp) cc_final: 0.8875 (tpp) REVERT: A 859 MET cc_start: 0.9220 (mtp) cc_final: 0.8640 (mmp) REVERT: A 1041 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7932 (pt) REVERT: A 1042 ASN cc_start: 0.8033 (p0) cc_final: 0.7734 (p0) REVERT: A 1043 MET cc_start: 0.9316 (ptt) cc_final: 0.8875 (pmm) REVERT: A 1078 ARG cc_start: 0.8672 (mtm110) cc_final: 0.8331 (ptm160) REVERT: B 171 MET cc_start: 0.8991 (tpp) cc_final: 0.8741 (tpp) REVERT: B 258 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8298 (t80) REVERT: B 416 ILE cc_start: 0.9370 (tt) cc_final: 0.9127 (mm) REVERT: B 450 SER cc_start: 0.9365 (t) cc_final: 0.8862 (p) REVERT: B 521 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B 542 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8216 (pp) REVERT: B 576 MET cc_start: 0.8271 (mtp) cc_final: 0.7965 (mtp) REVERT: B 587 MET cc_start: 0.8956 (tpt) cc_final: 0.8631 (tpt) REVERT: B 659 LYS cc_start: 0.8978 (tttt) cc_final: 0.8576 (ttmm) REVERT: B 750 LYS cc_start: 0.9277 (mttt) cc_final: 0.8904 (mttp) REVERT: B 781 CYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8172 (m) REVERT: B 813 ASP cc_start: 0.9030 (m-30) cc_final: 0.8762 (t0) REVERT: B 876 MET cc_start: 0.8642 (ttp) cc_final: 0.8310 (tmm) REVERT: B 1055 ASN cc_start: 0.9189 (m110) cc_final: 0.8784 (t0) REVERT: B 1059 PHE cc_start: 0.9301 (t80) cc_final: 0.9084 (t80) outliers start: 36 outliers final: 29 residues processed: 205 average time/residue: 0.2446 time to fit residues: 79.8096 Evaluate side-chains 201 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 781 CYS Chi-restraints excluded: chain B residue 910 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 148 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071578 restraints weight = 40408.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.074627 restraints weight = 19210.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076704 restraints weight = 11893.073| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13845 Z= 0.135 Angle : 0.669 12.668 18880 Z= 0.311 Chirality : 0.043 0.306 2229 Planarity : 0.003 0.038 2326 Dihedral : 7.456 70.213 2099 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.90 % Allowed : 29.16 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1731 helix: 2.26 (0.17), residues: 953 sheet: -0.36 (0.43), residues: 131 loop : -1.18 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 607 HIS 0.005 0.001 HIS B 853 PHE 0.022 0.001 PHE B1059 TYR 0.015 0.001 TYR A 186 ARG 0.002 0.000 ARG A1074 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 4) link_NAG-ASN : angle 1.01894 ( 12) link_BETA1-4 : bond 0.00753 ( 4) link_BETA1-4 : angle 3.20245 ( 12) hydrogen bonds : bond 0.03976 ( 764) hydrogen bonds : angle 3.81975 ( 2211) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.52109 ( 12) covalent geometry : bond 0.00309 (13831) covalent geometry : angle 0.66340 (18844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4620.41 seconds wall clock time: 82 minutes 16.42 seconds (4936.42 seconds total)