Starting phenix.real_space_refine on Thu Sep 26 18:06:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/09_2024/7fh1_31584.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/09_2024/7fh1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/09_2024/7fh1_31584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/09_2024/7fh1_31584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/09_2024/7fh1_31584.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fh1_31584/09_2024/7fh1_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.49, per 1000 atoms: 0.62 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: 3.58 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: 1.50 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: 4.49 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.00 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: 0.790 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.630 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- 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 13992 Z= 0.593 Angle : 1.203 32.967 19034 Z= 0.702 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 *********************** 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 fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 1.604 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: 0.2819 time to fit residues: 82.1037 Evaluate side-chains 132 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.0570 chunk 158 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13992 Z= 0.223 Angle : 0.831 14.850 19034 Z= 0.394 Chirality : 0.051 0.463 2242 Planarity : 0.007 0.100 2374 Dihedral : 18.255 103.821 2392 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.29 % Allowed : 11.25 % Favored : 86.46 % 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: -2.85 (0.19), residues: 1728 helix: -0.19 (0.21), residues: 644 sheet: -2.39 (0.28), residues: 242 loop : -3.21 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 346 HIS 0.003 0.001 HIS B 133 PHE 0.021 0.002 PHE B 637 TYR 0.017 0.002 TYR A 932 ARG 0.003 0.000 ARG B 208 *********************** 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 150 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 772 MET cc_start: 0.5604 (mmt) cc_final: 0.5338 (mmp) REVERT: A 775 ILE cc_start: 0.7633 (mm) cc_final: 0.7407 (tp) REVERT: B 363 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7681 (mmt90) REVERT: B 775 ILE cc_start: 0.7617 (mm) cc_final: 0.7403 (tp) outliers start: 32 outliers final: 15 residues processed: 141 average time/residue: 0.2415 time to fit residues: 51.5101 Evaluate side-chains 120 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 835 ILE 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 835 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.0370 overall best weight: 1.0462 ------------------------------------------------------------------------------- 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 179 ASN A 935 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13992 Z= 0.212 Angle : 0.721 11.125 19034 Z= 0.343 Chirality : 0.047 0.302 2242 Planarity : 0.005 0.099 2374 Dihedral : 15.161 103.741 2338 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.08 % Allowed : 13.25 % Favored : 84.67 % 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: -2.23 (0.20), residues: 1728 helix: 0.38 (0.21), residues: 658 sheet: -1.99 (0.29), residues: 238 loop : -2.98 (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 0.015 0.001 TYR B 843 ARG 0.006 0.000 ARG A 182 *********************** 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 148 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 775 ILE cc_start: 0.7747 (mm) cc_final: 0.7480 (tp) REVERT: B 775 ILE cc_start: 0.7732 (mm) cc_final: 0.7480 (tp) outliers start: 29 outliers final: 18 residues processed: 141 average time/residue: 0.2067 time to fit residues: 46.4105 Evaluate side-chains 125 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 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 751 PHE 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 156 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 678 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13992 Z= 0.353 Angle : 0.766 11.976 19034 Z= 0.370 Chirality : 0.049 0.382 2242 Planarity : 0.005 0.098 2374 Dihedral : 13.428 104.233 2328 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.94 % Allowed : 14.68 % Favored : 82.38 % 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: -1.93 (0.20), residues: 1728 helix: 0.70 (0.21), residues: 660 sheet: -1.81 (0.31), residues: 240 loop : -2.90 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 346 HIS 0.004 0.001 HIS A 626 PHE 0.021 0.002 PHE B 637 TYR 0.015 0.001 TYR B 932 ARG 0.008 0.001 ARG A 182 *********************** 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 149 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 775 ILE cc_start: 0.7848 (mm) cc_final: 0.7608 (tp) REVERT: B 775 ILE cc_start: 0.7850 (mm) cc_final: 0.7613 (tp) outliers start: 41 outliers final: 28 residues processed: 145 average time/residue: 0.2063 time to fit residues: 48.1313 Evaluate side-chains 128 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 612 TYR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 982 ASN 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 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 95 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN B 69 GLN B 480 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13992 Z= 0.156 Angle : 0.682 10.643 19034 Z= 0.322 Chirality : 0.045 0.298 2242 Planarity : 0.005 0.097 2374 Dihedral : 11.834 98.924 2328 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.01 % Allowed : 16.40 % Favored : 81.59 % 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: -1.61 (0.20), residues: 1728 helix: 1.08 (0.21), residues: 654 sheet: -1.30 (0.32), residues: 228 loop : -2.90 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 346 HIS 0.005 0.001 HIS B 626 PHE 0.014 0.001 PHE A 884 TYR 0.011 0.001 TYR B 492 ARG 0.009 0.000 ARG A 182 *********************** 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 136 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: A 359 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: A 914 MET cc_start: 0.7580 (pmm) cc_final: 0.7320 (pmm) REVERT: B 69 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8403 (mp10) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 0.2153 time to fit residues: 43.4762 Evaluate side-chains 122 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN 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 369 SER 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 564 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 69 GLN 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 612 TYR Chi-restraints excluded: chain B residue 751 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 139 optimal weight: 0.1980 chunk 77 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 765 GLN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13992 Z= 0.308 Angle : 0.716 11.368 19034 Z= 0.342 Chirality : 0.047 0.320 2242 Planarity : 0.005 0.099 2374 Dihedral : 11.213 98.227 2328 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.15 % Allowed : 17.84 % Favored : 80.01 % 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: -1.56 (0.20), residues: 1728 helix: 1.18 (0.21), residues: 658 sheet: -1.54 (0.32), residues: 240 loop : -2.87 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.017 0.001 PHE B 884 TYR 0.014 0.001 TYR A 932 ARG 0.011 0.001 ARG A 182 *********************** 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 fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.485 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 123 average time/residue: 0.2006 time to fit residues: 39.8974 Evaluate side-chains 115 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 369 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 938 THR 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 431 SER 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 775 ILE 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 18 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13992 Z= 0.159 Angle : 0.660 10.296 19034 Z= 0.311 Chirality : 0.044 0.284 2242 Planarity : 0.005 0.095 2374 Dihedral : 9.991 88.713 2324 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.72 % Allowed : 18.62 % Favored : 79.66 % 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: -1.39 (0.20), residues: 1728 helix: 1.36 (0.21), residues: 656 sheet: -1.15 (0.32), residues: 224 loop : -2.88 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.016 0.001 PHE B 884 TYR 0.010 0.001 TYR A 932 ARG 0.010 0.000 ARG A 182 *********************** 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 126 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.518 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 120 average time/residue: 0.2192 time to fit residues: 41.4890 Evaluate side-chains 111 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 415 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 184 CYS 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 775 ILE Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 chunk 152 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13992 Z= 0.191 Angle : 0.658 10.582 19034 Z= 0.311 Chirality : 0.045 0.290 2242 Planarity : 0.005 0.098 2374 Dihedral : 9.199 75.940 2324 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.08 % Allowed : 18.77 % Favored : 79.15 % 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: -1.23 (0.20), residues: 1728 helix: 1.55 (0.21), residues: 646 sheet: -1.08 (0.32), residues: 230 loop : -2.79 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.004 0.001 HIS B 626 PHE 0.015 0.001 PHE B 884 TYR 0.024 0.001 TYR B 874 ARG 0.014 0.000 ARG B 182 *********************** 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 fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.454 Fit side-chains REVERT: A 884 PHE cc_start: 0.7384 (t80) cc_final: 0.7136 (t80) outliers start: 29 outliers final: 21 residues processed: 114 average time/residue: 0.2243 time to fit residues: 39.9446 Evaluate side-chains 112 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 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 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 878 ASN 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 775 ILE Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 179 ASN A 878 ASN B 69 GLN B 878 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13992 Z= 0.256 Angle : 0.685 11.011 19034 Z= 0.327 Chirality : 0.045 0.284 2242 Planarity : 0.005 0.095 2374 Dihedral : 8.662 58.523 2324 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % 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: -1.22 (0.20), residues: 1728 helix: 1.56 (0.21), residues: 646 sheet: -1.06 (0.33), residues: 230 loop : -2.79 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 346 HIS 0.004 0.001 HIS B 626 PHE 0.016 0.001 PHE B 884 TYR 0.012 0.001 TYR A 932 ARG 0.012 0.000 ARG A 182 *********************** 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 122 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.538 Fit side-chains REVERT: A 884 PHE cc_start: 0.7449 (t80) cc_final: 0.7179 (t80) REVERT: B 884 PHE cc_start: 0.7406 (t80) cc_final: 0.7137 (t80) outliers start: 25 outliers final: 23 residues processed: 114 average time/residue: 0.2040 time to fit residues: 37.7089 Evaluate side-chains 114 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 360 THR 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 772 MET Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 878 ASN 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 611 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 842 HIS B 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13992 Z= 0.288 Angle : 0.688 11.220 19034 Z= 0.332 Chirality : 0.046 0.279 2242 Planarity : 0.005 0.096 2374 Dihedral : 8.256 58.474 2324 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.79 % Allowed : 19.13 % Favored : 79.08 % 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: -1.19 (0.20), residues: 1728 helix: 1.63 (0.21), residues: 646 sheet: -1.10 (0.33), residues: 230 loop : -2.80 (0.18), residues: 852 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 884 TYR 0.025 0.001 TYR B 874 ARG 0.013 0.000 ARG B 182 ********************** 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 fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.594 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 119 average time/residue: 0.2112 time to fit residues: 40.2411 Evaluate side-chains 118 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 360 THR 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 596 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 835 ILE 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 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 611 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 775 ILE 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 42 optimal weight: 0.7980 chunk 127 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 HIS A 878 ASN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.075320 restraints weight = 23383.521| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.43 r_work: 0.2648 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13992 Z= 0.172 Angle : 0.649 10.586 19034 Z= 0.310 Chirality : 0.044 0.267 2242 Planarity : 0.005 0.096 2374 Dihedral : 7.550 58.659 2324 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.65 % Allowed : 19.20 % Favored : 79.15 % 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: -1.01 (0.20), residues: 1728 helix: 1.79 (0.21), residues: 650 sheet: -1.03 (0.33), residues: 230 loop : -2.72 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 346 HIS 0.006 0.001 HIS A 842 PHE 0.011 0.001 PHE B 697 TYR 0.010 0.001 TYR B 932 ARG 0.016 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.84 seconds wall clock time: 47 minutes 32.31 seconds (2852.31 seconds total)