Starting phenix.real_space_refine on Thu Jul 31 18:49:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fh1_31584/07_2025/7fh1_31584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fh1_31584/07_2025/7fh1_31584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2025/7fh1_31584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2025/7fh1_31584.map" model { file = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2025/7fh1_31584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fh1_31584/07_2025/7fh1_31584.cif" } resolution = 3.34 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 8834 2.51 5 N 2246 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 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: 13672 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6691 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 30, 'TRANS': 843} Chain breaks: 4 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 6691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6691 Classifications: {'peptide': 874} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 30, 'TRANS': 843} Chain breaks: 4 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 196 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.54, per 1000 atoms: 0.92 Number of scatterers: 13672 At special positions: 0 Unit cell: (96.743, 79.351, 170.659, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2500 8.00 N 2246 7.00 C 8834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 268 " distance=2.04 Simple disulfide: pdb=" SG CYS A 357 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 184 " distance=2.04 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 268 " distance=2.04 Simple disulfide: pdb=" SG CYS B 357 " - pdb=" SG CYS B 378 " 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 BETA1-3 " BMA F 3 " - " BMA F 4 " " BMA J 3 " - " BMA J 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " BETA1-6 " BMA F 3 " - " BMA F 5 " " BMA J 3 " - " BMA J 5 " Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 24 sheets defined 40.1% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.531A pdb=" N ALA A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.686A pdb=" N CYS A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.642A pdb=" N LEU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 518 through 549 removed outlier: 3.981A pdb=" N VAL A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 592 removed outlier: 3.542A pdb=" N VAL A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 574 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 633 removed outlier: 4.024A pdb=" N CYS A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 680 removed outlier: 5.047A pdb=" N PHE A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 701 removed outlier: 3.578A pdb=" N LEU A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.791A pdb=" N LEU A 709 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 758 removed outlier: 3.648A pdb=" N ALA A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 772 removed outlier: 3.604A pdb=" N ASP A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 845 removed outlier: 3.543A pdb=" N ARG A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 886 removed outlier: 3.989A pdb=" N MET A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.959A pdb=" N VAL A 930 " --> pdb=" O PHE A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 946 removed outlier: 4.182A pdb=" N LEU A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 954 removed outlier: 3.927A pdb=" N LEU A 952 " --> pdb=" O CYS A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 987 removed outlier: 3.510A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.531A pdb=" N ALA B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 242 through 256 removed outlier: 3.686A pdb=" N CYS B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.551A pdb=" N LEU B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 518 through 549 removed outlier: 3.981A pdb=" N VAL B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 592 removed outlier: 3.542A pdb=" N VAL B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL B 574 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 633 removed outlier: 4.025A pdb=" N CYS B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 680 removed outlier: 5.047A pdb=" N PHE B 672 " --> pdb=" O TRP B 668 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 675 " --> pdb=" O TYR B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.578A pdb=" N LEU B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 709 removed outlier: 3.791A pdb=" N LEU B 709 " --> pdb=" O ASN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 758 removed outlier: 3.648A pdb=" N ALA B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 772 removed outlier: 3.605A pdb=" N ASP B 768 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 771 " --> pdb=" O VAL B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 845 removed outlier: 3.543A pdb=" N ARG B 845 " --> pdb=" O GLN B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 886 removed outlier: 3.989A pdb=" N MET B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 882 " --> pdb=" O ASN B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.959A pdb=" N VAL B 930 " --> pdb=" O PHE B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 946 removed outlier: 4.182A pdb=" N LEU B 939 " --> pdb=" O ASN B 935 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 954 removed outlier: 3.927A pdb=" N LEU B 952 " --> pdb=" O CYS B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 987 removed outlier: 3.510A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 980 " --> pdb=" O ASN B 976 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 985 " --> pdb=" O LYS B 981 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 88 removed outlier: 7.032A pdb=" N ILE A 96 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA6, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.557A pdb=" N ARG A 213 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 221 " --> pdb=" O ARG A 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 332 through 337 Processing sheet with id=AB1, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AB2, first strand: chain 'A' and resid 445 through 446 removed outlier: 3.530A pdb=" N ARG A 463 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 491 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 635 through 639 removed outlier: 3.768A pdb=" N ASP A 635 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 831 through 833 removed outlier: 7.325A pdb=" N LYS A 897 " --> pdb=" O ASN A 921 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 88 removed outlier: 7.031A pdb=" N ILE B 96 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AB9, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AC1, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AC2, first strand: chain 'B' and resid 213 through 214 removed outlier: 3.557A pdb=" N ARG B 213 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 221 " --> pdb=" O ARG B 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AC4, first strand: chain 'B' and resid 445 through 446 removed outlier: 3.530A pdb=" N ARG B 463 " --> pdb=" O ASP B 446 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA B 491 " --> pdb=" O THR B 466 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 635 through 639 removed outlier: 3.768A pdb=" N ASP B 635 " --> pdb=" O LEU B 780 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 831 through 833 removed outlier: 7.325A pdb=" N LYS B 897 " --> pdb=" O ASN B 921 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1506 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: 4.77 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3665 1.33 - 1.45: 2800 1.45 - 1.57: 7402 1.57 - 1.70: 1 1.70 - 1.82: 124 Bond restraints: 13992 Sorted by residual: bond pdb=" C2 BMA F 5 " pdb=" C3 BMA F 5 " ideal model delta sigma weight residual 1.544 1.486 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.576 -0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" C GLN A 747 " pdb=" O GLN A 747 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.31e+00 bond pdb=" C GLN B 747 " pdb=" O GLN B 747 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.31e+00 bond pdb=" CA VAL B 415 " pdb=" C VAL B 415 " ideal model delta sigma weight residual 1.522 1.546 -0.024 1.21e-02 6.83e+03 3.97e+00 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.59: 18969 6.59 - 13.19: 49 13.19 - 19.78: 12 19.78 - 26.37: 2 26.37 - 32.97: 2 Bond angle restraints: 19034 Sorted by residual: angle pdb=" N PHE A 758 " pdb=" CA PHE A 758 " pdb=" C PHE A 758 " ideal model delta sigma weight residual 114.09 147.06 -32.97 1.55e+00 4.16e-01 4.52e+02 angle pdb=" N PHE B 758 " pdb=" CA PHE B 758 " pdb=" C PHE B 758 " ideal model delta sigma weight residual 114.09 147.00 -32.91 1.55e+00 4.16e-01 4.51e+02 angle pdb=" C PHE B 758 " pdb=" CA PHE B 758 " pdb=" CB PHE B 758 " ideal model delta sigma weight residual 109.80 87.15 22.65 1.61e+00 3.86e-01 1.98e+02 angle pdb=" C PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta sigma weight residual 109.80 87.15 22.65 1.61e+00 3.86e-01 1.98e+02 angle pdb=" C VAL B 613 " pdb=" CA VAL B 613 " pdb=" CB VAL B 613 " ideal model delta sigma weight residual 111.65 92.03 19.62 1.41e+00 5.03e-01 1.94e+02 ... (remaining 19029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 7869 26.91 - 53.82: 485 53.82 - 80.73: 91 80.73 - 107.63: 42 107.63 - 134.54: 35 Dihedral angle restraints: 8522 sinusoidal: 3420 harmonic: 5102 Sorted by residual: dihedral pdb=" C PHE B 758 " pdb=" N PHE B 758 " pdb=" CA PHE B 758 " pdb=" CB PHE B 758 " ideal model delta harmonic sigma weight residual -122.60 -93.04 -29.56 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" C PHE A 758 " pdb=" N PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta harmonic sigma weight residual -122.60 -93.05 -29.55 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" N PHE A 758 " pdb=" C PHE A 758 " pdb=" CA PHE A 758 " pdb=" CB PHE A 758 " ideal model delta harmonic sigma weight residual 122.80 95.48 27.32 0 2.50e+00 1.60e-01 1.19e+02 ... (remaining 8519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2208 0.163 - 0.327: 26 0.327 - 0.490: 2 0.490 - 0.654: 3 0.654 - 0.817: 3 Chirality restraints: 2242 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA J 5 " pdb=" O6 BMA J 3 " pdb=" C2 BMA J 5 " pdb=" O5 BMA J 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.43e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.63e+02 ... (remaining 2239 not shown) Planarity restraints: 2374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG D 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.348 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG H 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG E 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.517 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.200 2.00e-02 2.50e+03 ... (remaining 2371 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1772 2.74 - 3.28: 13660 3.28 - 3.82: 20522 3.82 - 4.36: 24304 4.36 - 4.90: 43090 Nonbonded interactions: 103348 Sorted by model distance: nonbonded pdb=" C VAL B 613 " pdb=" CG1 VAL B 613 " model vdw 2.200 2.952 nonbonded pdb=" C VAL A 613 " pdb=" CG1 VAL A 613 " model vdw 2.201 2.952 nonbonded pdb=" ND2 ASN B 242 " pdb=" C1 NAG J 1 " model vdw 2.206 3.550 nonbonded pdb=" O GLY A 91 " pdb=" OD1 ASN B 242 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASN A 242 " pdb=" O GLY B 91 " model vdw 2.214 3.040 ... (remaining 103343 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 44.390 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.061 14030 Z= 0.388 Angle : 1.254 41.948 19124 Z= 0.711 Chirality : 0.069 0.817 2242 Planarity : 0.019 0.305 2374 Dihedral : 21.248 134.542 5158 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 3.15 % Allowed : 2.22 % Favored : 94.63 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % 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: -3.88 (0.18), residues: 1728 helix: -1.40 (0.20), residues: 626 sheet: -2.95 (0.29), residues: 232 loop : -3.45 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 346 HIS 0.007 0.002 HIS A 473 PHE 0.027 0.002 PHE B 895 TYR 0.020 0.002 TYR B 932 ARG 0.008 0.001 ARG A 975 Details of bonding type rmsd link_BETA1-4 : bond 0.00472 ( 10) link_BETA1-4 : angle 2.74868 ( 30) hydrogen bonds : bond 0.25827 ( 530) hydrogen bonds : angle 8.87909 ( 1506) link_BETA1-6 : bond 0.04176 ( 2) link_BETA1-6 : angle 18.90862 ( 6) SS BOND : bond 0.00507 ( 24) SS BOND : angle 1.70563 ( 48) link_BETA1-3 : bond 0.01176 ( 2) link_BETA1-3 : angle 1.35265 ( 6) covalent geometry : bond 0.00914 (13992) covalent geometry : angle 1.20330 (19034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 604 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7791 (mm) REVERT: A 608 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6470 (tpt-90) REVERT: A 669 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6680 (ptp-110) REVERT: A 775 ILE cc_start: 0.7596 (mm) cc_final: 0.7349 (mm) REVERT: B 604 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7814 (mm) REVERT: B 608 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6480 (tpt-90) REVERT: B 669 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6601 (ptp-110) REVERT: B 775 ILE cc_start: 0.7576 (mm) cc_final: 0.7342 (mm) outliers start: 44 outliers final: 25 residues processed: 205 average time/residue: 0.2807 time to fit residues: 81.7822 Evaluate side-chains 132 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 669 ARG Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 936 GLU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 608 ARG Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 869 GLN Chi-restraints excluded: chain B residue 936 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 179 ASN A 242 ASN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS B 69 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 242 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.074693 restraints weight = 23026.836| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.69 r_work: 0.2717 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14030 Z= 0.169 Angle : 0.872 15.339 19124 Z= 0.407 Chirality : 0.051 0.467 2242 Planarity : 0.007 0.100 2374 Dihedral : 17.959 102.955 2392 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.51 % Allowed : 11.25 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -2.84 (0.19), residues: 1728 helix: -0.17 (0.21), residues: 644 sheet: -2.39 (0.28), residues: 242 loop : -3.22 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 346 HIS 0.004 0.001 HIS B 133 PHE 0.021 0.002 PHE B 637 TYR 0.017 0.002 TYR A 932 ARG 0.003 0.001 ARG B 208 Details of bonding type rmsd link_BETA1-4 : bond 0.01325 ( 10) link_BETA1-4 : angle 3.75142 ( 30) hydrogen bonds : bond 0.05317 ( 530) hydrogen bonds : angle 5.01157 ( 1506) link_BETA1-6 : bond 0.00805 ( 2) link_BETA1-6 : angle 4.77716 ( 6) SS BOND : bond 0.00292 ( 24) SS BOND : angle 1.76035 ( 48) link_BETA1-3 : bond 0.00643 ( 2) link_BETA1-3 : angle 3.36622 ( 6) covalent geometry : bond 0.00381 (13992) covalent geometry : angle 0.85056 (19034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 772 MET cc_start: 0.5909 (mmt) cc_final: 0.5660 (mmp) REVERT: B 363 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7897 (mmt90) REVERT: B 877 MET cc_start: 0.8756 (ttm) cc_final: 0.8415 (tpp) outliers start: 35 outliers final: 19 residues processed: 146 average time/residue: 0.2581 time to fit residues: 57.1687 Evaluate side-chains 126 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 70 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 0.0870 chunk 59 optimal weight: 0.0270 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 0.0370 overall best weight: 0.8296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 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 = 0.3541 r_free = 0.3541 target = 0.116297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.075219 restraints weight = 23467.166| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.70 r_work: 0.2729 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14030 Z= 0.128 Angle : 0.730 11.028 19124 Z= 0.343 Chirality : 0.047 0.302 2242 Planarity : 0.005 0.099 2374 Dihedral : 15.195 103.419 2344 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.08 % Allowed : 14.04 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -2.17 (0.20), residues: 1728 helix: 0.48 (0.21), residues: 654 sheet: -1.88 (0.29), residues: 242 loop : -3.01 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.003 0.001 HIS B 473 PHE 0.014 0.001 PHE B 785 TYR 0.017 0.001 TYR A 733 ARG 0.006 0.001 ARG A 182 Details of bonding type rmsd link_BETA1-4 : bond 0.01368 ( 10) link_BETA1-4 : angle 3.65558 ( 30) hydrogen bonds : bond 0.04144 ( 530) hydrogen bonds : angle 4.45413 ( 1506) link_BETA1-6 : bond 0.00964 ( 2) link_BETA1-6 : angle 4.14298 ( 6) SS BOND : bond 0.00449 ( 24) SS BOND : angle 1.48202 ( 48) link_BETA1-3 : bond 0.01132 ( 2) link_BETA1-3 : angle 2.00935 ( 6) covalent geometry : bond 0.00284 (13992) covalent geometry : angle 0.70891 (19034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.388 Fit side-chains REVERT: A 746 ILE cc_start: 0.9239 (mm) cc_final: 0.9020 (mt) REVERT: A 877 MET cc_start: 0.8393 (tpp) cc_final: 0.8181 (tpt) REVERT: A 884 PHE cc_start: 0.8668 (t80) cc_final: 0.8321 (t80) REVERT: B 637 PHE cc_start: 0.6855 (t80) cc_final: 0.6633 (t80) REVERT: B 746 ILE cc_start: 0.9268 (mm) cc_final: 0.9046 (mt) REVERT: B 877 MET cc_start: 0.8655 (ttm) cc_final: 0.8342 (tpt) outliers start: 29 outliers final: 19 residues processed: 135 average time/residue: 0.2107 time to fit residues: 45.9878 Evaluate side-chains 124 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 878 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 678 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.071841 restraints weight = 23542.556| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.69 r_work: 0.2667 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14030 Z= 0.178 Angle : 0.751 11.551 19124 Z= 0.354 Chirality : 0.048 0.365 2242 Planarity : 0.005 0.098 2374 Dihedral : 13.190 102.521 2328 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.79 % Allowed : 15.33 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -1.87 (0.20), residues: 1728 helix: 0.74 (0.21), residues: 660 sheet: -1.68 (0.31), residues: 244 loop : -2.89 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 346 HIS 0.004 0.001 HIS A 626 PHE 0.024 0.001 PHE A 637 TYR 0.015 0.001 TYR B 932 ARG 0.004 0.000 ARG B 440 Details of bonding type rmsd link_BETA1-4 : bond 0.01321 ( 10) link_BETA1-4 : angle 3.91560 ( 30) hydrogen bonds : bond 0.04280 ( 530) hydrogen bonds : angle 4.24261 ( 1506) link_BETA1-6 : bond 0.00844 ( 2) link_BETA1-6 : angle 3.65553 ( 6) SS BOND : bond 0.00200 ( 24) SS BOND : angle 1.57714 ( 48) link_BETA1-3 : bond 0.01129 ( 2) link_BETA1-3 : angle 1.75007 ( 6) covalent geometry : bond 0.00431 (13992) covalent geometry : angle 0.72822 (19034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 1.596 Fit side-chains REVERT: A 675 ASN cc_start: 0.7936 (t0) cc_final: 0.7726 (t0) REVERT: A 746 ILE cc_start: 0.9244 (mm) cc_final: 0.9032 (mt) REVERT: B 637 PHE cc_start: 0.6683 (t80) cc_final: 0.6441 (t80) REVERT: B 675 ASN cc_start: 0.7965 (t0) cc_final: 0.7761 (t0) REVERT: B 746 ILE cc_start: 0.9251 (mm) cc_final: 0.9036 (mt) REVERT: B 877 MET cc_start: 0.8660 (ttm) cc_final: 0.8425 (tpt) REVERT: B 925 TYR cc_start: 0.7855 (m-80) cc_final: 0.7468 (m-80) outliers start: 39 outliers final: 27 residues processed: 135 average time/residue: 0.2038 time to fit residues: 45.3767 Evaluate side-chains 126 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 982 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 0 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 129 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.070449 restraints weight = 23448.434| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.66 r_work: 0.2632 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14030 Z= 0.200 Angle : 0.754 11.835 19124 Z= 0.357 Chirality : 0.048 0.320 2242 Planarity : 0.005 0.097 2374 Dihedral : 11.893 101.534 2328 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.44 % Allowed : 16.98 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -1.70 (0.20), residues: 1728 helix: 0.98 (0.21), residues: 660 sheet: -1.60 (0.32), residues: 240 loop : -2.89 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.015 0.001 PHE A 609 TYR 0.014 0.001 TYR A 932 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd link_BETA1-4 : bond 0.01195 ( 10) link_BETA1-4 : angle 4.08784 ( 30) hydrogen bonds : bond 0.04392 ( 530) hydrogen bonds : angle 4.17724 ( 1506) link_BETA1-6 : bond 0.00850 ( 2) link_BETA1-6 : angle 3.39951 ( 6) SS BOND : bond 0.00337 ( 24) SS BOND : angle 1.62612 ( 48) link_BETA1-3 : bond 0.01203 ( 2) link_BETA1-3 : angle 1.71316 ( 6) covalent geometry : bond 0.00486 (13992) covalent geometry : angle 0.73078 (19034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.390 Fit side-chains REVERT: A 925 TYR cc_start: 0.7986 (m-80) cc_final: 0.7602 (m-80) REVERT: B 925 TYR cc_start: 0.7902 (m-80) cc_final: 0.7538 (m-80) REVERT: B 965 TYR cc_start: 0.9237 (t80) cc_final: 0.8937 (t80) outliers start: 34 outliers final: 26 residues processed: 130 average time/residue: 0.1958 time to fit residues: 41.2326 Evaluate side-chains 116 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 168 optimal weight: 0.0170 chunk 127 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.071138 restraints weight = 23709.555| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.77 r_work: 0.2656 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14030 Z= 0.131 Angle : 0.702 11.089 19124 Z= 0.329 Chirality : 0.046 0.302 2242 Planarity : 0.005 0.097 2374 Dihedral : 10.841 96.572 2324 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.51 % Allowed : 18.05 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -1.52 (0.20), residues: 1728 helix: 1.25 (0.21), residues: 654 sheet: -1.27 (0.32), residues: 230 loop : -2.94 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.039 0.001 PHE B 637 TYR 0.011 0.001 TYR A 932 ARG 0.010 0.000 ARG B 182 Details of bonding type rmsd link_BETA1-4 : bond 0.01204 ( 10) link_BETA1-4 : angle 3.99944 ( 30) hydrogen bonds : bond 0.03845 ( 530) hydrogen bonds : angle 4.03533 ( 1506) link_BETA1-6 : bond 0.01072 ( 2) link_BETA1-6 : angle 3.42424 ( 6) SS BOND : bond 0.00277 ( 24) SS BOND : angle 1.36606 ( 48) link_BETA1-3 : bond 0.01130 ( 2) link_BETA1-3 : angle 1.77030 ( 6) covalent geometry : bond 0.00302 (13992) covalent geometry : angle 0.67899 (19034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.448 Fit side-chains REVERT: B 925 TYR cc_start: 0.7976 (m-80) cc_final: 0.7581 (m-80) REVERT: B 965 TYR cc_start: 0.9171 (t80) cc_final: 0.8917 (t80) outliers start: 35 outliers final: 23 residues processed: 124 average time/residue: 0.2060 time to fit residues: 41.0906 Evaluate side-chains 110 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 70 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.0030 chunk 126 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.073529 restraints weight = 23542.044| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.75 r_work: 0.2705 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14030 Z= 0.112 Angle : 0.688 10.540 19124 Z= 0.323 Chirality : 0.044 0.288 2242 Planarity : 0.005 0.096 2374 Dihedral : 9.665 85.093 2324 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.22 % Allowed : 19.56 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -1.28 (0.20), residues: 1728 helix: 1.45 (0.21), residues: 658 sheet: -1.04 (0.32), residues: 234 loop : -2.86 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.015 0.001 PHE B 884 TYR 0.011 0.001 TYR B 492 ARG 0.002 0.000 ARG A 608 Details of bonding type rmsd link_BETA1-4 : bond 0.01275 ( 10) link_BETA1-4 : angle 3.91007 ( 30) hydrogen bonds : bond 0.03349 ( 530) hydrogen bonds : angle 3.88835 ( 1506) link_BETA1-6 : bond 0.01314 ( 2) link_BETA1-6 : angle 3.38260 ( 6) SS BOND : bond 0.00248 ( 24) SS BOND : angle 1.15940 ( 48) link_BETA1-3 : bond 0.01056 ( 2) link_BETA1-3 : angle 1.75083 ( 6) covalent geometry : bond 0.00240 (13992) covalent geometry : angle 0.66638 (19034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.464 Fit side-chains REVERT: B 691 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8403 (tp-100) REVERT: B 925 TYR cc_start: 0.7984 (m-80) cc_final: 0.7612 (m-80) outliers start: 31 outliers final: 17 residues processed: 128 average time/residue: 0.2322 time to fit residues: 45.8988 Evaluate side-chains 108 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 878 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.070014 restraints weight = 23532.601| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.76 r_work: 0.2637 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14030 Z= 0.186 Angle : 0.719 11.325 19124 Z= 0.342 Chirality : 0.046 0.291 2242 Planarity : 0.005 0.097 2374 Dihedral : 9.239 74.644 2324 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.08 % Allowed : 19.20 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.20), residues: 1728 helix: 1.59 (0.21), residues: 648 sheet: -1.09 (0.33), residues: 230 loop : -2.87 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS B 626 PHE 0.015 0.001 PHE B 637 TYR 0.013 0.001 TYR B 932 ARG 0.013 0.000 ARG B 182 Details of bonding type rmsd link_BETA1-4 : bond 0.01154 ( 10) link_BETA1-4 : angle 4.01842 ( 30) hydrogen bonds : bond 0.03945 ( 530) hydrogen bonds : angle 3.93053 ( 1506) link_BETA1-6 : bond 0.01126 ( 2) link_BETA1-6 : angle 3.67590 ( 6) SS BOND : bond 0.00372 ( 24) SS BOND : angle 1.39873 ( 48) link_BETA1-3 : bond 0.01218 ( 2) link_BETA1-3 : angle 1.65060 ( 6) covalent geometry : bond 0.00448 (13992) covalent geometry : angle 0.69521 (19034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 1.706 Fit side-chains REVERT: A 359 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: B 925 TYR cc_start: 0.8023 (m-80) cc_final: 0.7653 (m-80) outliers start: 29 outliers final: 19 residues processed: 115 average time/residue: 0.2154 time to fit residues: 40.1178 Evaluate side-chains 110 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 37 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 0.0570 chunk 72 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.074691 restraints weight = 23296.280| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.21 r_work: 0.2620 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14030 Z= 0.126 Angle : 0.692 10.871 19124 Z= 0.323 Chirality : 0.044 0.279 2242 Planarity : 0.005 0.096 2374 Dihedral : 8.453 58.524 2324 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.79 % Allowed : 18.91 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -1.10 (0.20), residues: 1728 helix: 1.77 (0.21), residues: 646 sheet: -0.98 (0.33), residues: 230 loop : -2.83 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS A 626 PHE 0.014 0.001 PHE B 884 TYR 0.013 0.001 TYR B 932 ARG 0.001 0.000 ARG B 975 Details of bonding type rmsd link_BETA1-4 : bond 0.01318 ( 10) link_BETA1-4 : angle 3.78203 ( 30) hydrogen bonds : bond 0.03515 ( 530) hydrogen bonds : angle 3.83214 ( 1506) link_BETA1-6 : bond 0.01274 ( 2) link_BETA1-6 : angle 3.46992 ( 6) SS BOND : bond 0.00490 ( 24) SS BOND : angle 1.39934 ( 48) link_BETA1-3 : bond 0.01025 ( 2) link_BETA1-3 : angle 1.58983 ( 6) covalent geometry : bond 0.00290 (13992) covalent geometry : angle 0.66980 (19034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.457 Fit side-chains REVERT: A 359 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8755 (m-30) outliers start: 25 outliers final: 20 residues processed: 112 average time/residue: 0.2177 time to fit residues: 39.1838 Evaluate side-chains 112 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 938 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 115 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 133 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.076495 restraints weight = 23457.292| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.16 r_work: 0.2664 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14030 Z= 0.110 Angle : 0.654 10.484 19124 Z= 0.309 Chirality : 0.043 0.272 2242 Planarity : 0.005 0.096 2374 Dihedral : 7.348 58.718 2324 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.79 % Allowed : 18.98 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.85 (0.20), residues: 1728 helix: 2.00 (0.21), residues: 638 sheet: -0.89 (0.34), residues: 210 loop : -2.62 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS A 626 PHE 0.012 0.001 PHE B 884 TYR 0.011 0.001 TYR A 932 ARG 0.016 0.000 ARG B 182 Details of bonding type rmsd link_BETA1-4 : bond 0.01211 ( 10) link_BETA1-4 : angle 3.57817 ( 30) hydrogen bonds : bond 0.03153 ( 530) hydrogen bonds : angle 3.72689 ( 1506) link_BETA1-6 : bond 0.01432 ( 2) link_BETA1-6 : angle 2.45068 ( 6) SS BOND : bond 0.00285 ( 24) SS BOND : angle 1.18050 ( 48) link_BETA1-3 : bond 0.00737 ( 2) link_BETA1-3 : angle 1.75638 ( 6) covalent geometry : bond 0.00244 (13992) covalent geometry : angle 0.63453 (19034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.565 Fit side-chains REVERT: A 257 MET cc_start: 0.8596 (mmt) cc_final: 0.8365 (mmt) REVERT: A 359 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8757 (m-30) REVERT: A 671 TYR cc_start: 0.8392 (m-80) cc_final: 0.8127 (m-80) REVERT: B 257 MET cc_start: 0.8599 (mmt) cc_final: 0.8378 (mmt) REVERT: B 884 PHE cc_start: 0.8628 (t80) cc_final: 0.8226 (t80) outliers start: 25 outliers final: 20 residues processed: 120 average time/residue: 0.2095 time to fit residues: 40.9012 Evaluate side-chains 113 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 62 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 153 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 152 optimal weight: 0.0870 chunk 138 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN 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 = 0.116400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.077661 restraints weight = 23603.948| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.19 r_work: 0.2696 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14030 Z= 0.102 Angle : 0.649 10.216 19124 Z= 0.306 Chirality : 0.043 0.263 2242 Planarity : 0.005 0.095 2374 Dihedral : 7.106 58.546 2324 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.58 % Allowed : 19.63 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.79 (0.20), residues: 1728 helix: 2.01 (0.21), residues: 650 sheet: -0.87 (0.35), residues: 202 loop : -2.60 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 346 HIS 0.004 0.001 HIS A 626 PHE 0.016 0.001 PHE B 884 TYR 0.010 0.001 TYR B 932 ARG 0.001 0.000 ARG B 440 Details of bonding type rmsd link_BETA1-4 : bond 0.01236 ( 10) link_BETA1-4 : angle 3.55892 ( 30) hydrogen bonds : bond 0.03015 ( 530) hydrogen bonds : angle 3.67541 ( 1506) link_BETA1-6 : bond 0.01201 ( 2) link_BETA1-6 : angle 2.41689 ( 6) SS BOND : bond 0.00258 ( 24) SS BOND : angle 1.04423 ( 48) link_BETA1-3 : bond 0.00876 ( 2) link_BETA1-3 : angle 1.51316 ( 6) covalent geometry : bond 0.00220 (13992) covalent geometry : angle 0.63052 (19034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6142.88 seconds wall clock time: 106 minutes 13.50 seconds (6373.50 seconds total)