Starting phenix.real_space_refine on Sun May 25 19:47:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bio_44595/05_2025/9bio_44595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bio_44595/05_2025/9bio_44595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bio_44595/05_2025/9bio_44595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bio_44595/05_2025/9bio_44595.map" model { file = "/net/cci-nas-00/data/ceres_data/9bio_44595/05_2025/9bio_44595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bio_44595/05_2025/9bio_44595.cif" } resolution = 2.83 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= 0.011 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 141 5.16 5 C 17242 2.51 5 N 4433 2.21 5 O 5681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27498 Number of models: 1 Model: "" Number of chains: 68 Chain: "B" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1088 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "G" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3722 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain: "S" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "A" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1088 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3722 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "F" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Chain: "I" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "J" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1088 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3722 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain: "M" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "N" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "O" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Chain: "P" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "Q" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" 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: "T" 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: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "W" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 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: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "g" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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': 1, 'MAN': 2, '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: "k" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "l" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "m" 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: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" 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: "p" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "q" 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: "r" 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: "s" 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: "t" 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: "u" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "v" 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: "w" 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: "x" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, '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: "y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "0" 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: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" 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: "3" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "4" 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: "5" 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: "6" 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "U" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'NAG': 8, 'PO4': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" 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: "K" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.05, per 1000 atoms: 0.66 Number of scatterers: 27498 At special positions: 0 Unit cell: (158.935, 153.454, 137.013, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 P 1 15.00 O 5681 8.00 N 4433 7.00 C 17242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS K 501 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.04 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.04 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " 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 ALPHA1-2 " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " " MAN y 4 " - " MAN y 5 " " MAN y 5 " - " MAN y 6 " ALPHA1-3 " BMA 3 3 " - " MAN 3 7 " " MAN 3 4 " - " MAN 3 5 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " MAN W 7 " - " MAN W 8 " " BMA X 3 " - " MAN X 7 " " MAN X 4 " - " MAN X 5 " " BMA b 3 " - " MAN b 7 " " MAN b 4 " - " MAN b 5 " " BMA g 3 " - " MAN g 6 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 4 " " MAN k 7 " - " MAN k 8 " " BMA l 3 " - " MAN l 7 " " MAN l 4 " - " MAN l 5 " " BMA p 3 " - " MAN p 7 " " MAN p 4 " - " MAN p 5 " " BMA u 3 " - " MAN u 6 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " MAN y 7 " - " MAN y 8 " " BMA z 3 " - " MAN z 7 " " MAN z 4 " - " MAN z 5 " ALPHA1-6 " BMA 3 3 " - " MAN 3 4 " " MAN 3 4 " - " MAN 3 6 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 5 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 7 " " MAN W 7 " - " MAN W 9 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 6 " " BMA b 3 " - " MAN b 4 " " MAN b 4 " - " MAN b 6 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " " BMA j 3 " - " MAN j 5 " " BMA k 3 " - " MAN k 7 " " MAN k 7 " - " MAN k 9 " " BMA l 3 " - " MAN l 4 " " MAN l 4 " - " MAN l 6 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 6 " " BMA u 3 " - " MAN u 4 " " MAN u 4 " - " MAN u 5 " " BMA x 3 " - " MAN x 5 " " BMA y 3 " - " MAN y 7 " " MAN y 7 " - " MAN y 9 " " BMA z 3 " - " MAN z 4 " " MAN z 4 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " 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 g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG Q 1 " - " FUC Q 7 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG g 1 " - " FUC g 7 " " NAG u 1 " - " FUC u 7 " NAG-ASN " NAG 0 1 " - " ASN K 295 " " NAG 1 1 " - " ASN K 386 " " NAG 2 1 " - " ASN K 448 " " NAG 3 1 " - " ASN K 88 " " NAG 4 1 " - " ASN K 334 " " NAG 5 1 " - " ASN K 241 " " NAG 6 1 " - " ASN K 289 " " NAG A 701 " - " ASN A 616 " " NAG A 702 " - " ASN A 611 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 611 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 149 " " NAG C 607 " - " ASN C 356 " " NAG C 608 " - " ASN C 405 " " NAG C 609 " - " ASN C 339 " " NAG E 301 " - " ASN E 72 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 234 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 392 " " NAG G 605 " - " ASN G 149 " " NAG G 606 " - " ASN G 356 " " NAG G 607 " - " ASN G 405 " " NAG G 608 " - " ASN G 339 " " NAG J 701 " - " ASN J 616 " " NAG J 702 " - " ASN J 611 " " NAG K 601 " - " ASN K 133 " " NAG K 602 " - " ASN K 234 " " NAG K 603 " - " ASN K 301 " " NAG K 604 " - " ASN K 392 " " NAG K 605 " - " ASN K 149 " " NAG K 606 " - " ASN K 356 " " NAG K 607 " - " ASN K 405 " " NAG K 608 " - " ASN K 339 " " NAG N 301 " - " ASN N 72 " " NAG Q 1 " - " ASN B 625 " " NAG R 1 " - " ASN G 156 " " NAG T 1 " - " ASN G 160 " " NAG U 301 " - " ASN U 72 " " NAG V 1 " - " ASN G 197 " " NAG W 1 " - " ASN G 262 " " NAG X 1 " - " ASN G 276 " " NAG Y 1 " - " ASN G 295 " " NAG Z 1 " - " ASN G 386 " " NAG a 1 " - " ASN G 448 " " NAG b 1 " - " ASN G 88 " " NAG c 1 " - " ASN G 334 " " NAG d 1 " - " ASN G 241 " " NAG e 1 " - " ASN G 289 " " NAG f 1 " - " ASN A 637 " " NAG g 1 " - " ASN A 625 " " NAG h 1 " - " ASN C 156 " " NAG i 1 " - " ASN C 160 " " NAG j 1 " - " ASN C 197 " " NAG k 1 " - " ASN C 262 " " NAG l 1 " - " ASN C 276 " " NAG m 1 " - " ASN C 295 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 448 " " NAG p 1 " - " ASN C 88 " " NAG q 1 " - " ASN C 334 " " NAG r 1 " - " ASN C 241 " " NAG s 1 " - " ASN C 289 " " NAG t 1 " - " ASN J 637 " " NAG u 1 " - " ASN J 625 " " NAG v 1 " - " ASN K 156 " " NAG w 1 " - " ASN K 160 " " NAG x 1 " - " ASN K 197 " " NAG y 1 " - " ASN K 262 " " NAG z 1 " - " ASN K 276 " Time building additional restraints: 9.63 Conformation dependent library (CDL) restraints added in 3.4 seconds 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 48 sheets defined 16.6% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.938A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 551 removed outlier: 3.661A pdb=" N GLN B 550 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 removed outlier: 3.707A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.552A pdb=" N ASN B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.503A pdb=" N ASP B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.966A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 126 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.507A pdb=" N VAL G 346 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU G 351 " --> pdb=" O GLY G 347 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 459B through 463 Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.640A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.517A pdb=" N TYR S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.832A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.235A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.974A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.559A pdb=" N GLN A 550 " --> pdb=" O GLY A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.630A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.514A pdb=" N ASN A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.543A pdb=" N ASP A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.008A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.570A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 459B through 463 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.507A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.522A pdb=" N ASP D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.786A pdb=" N PHE I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.163A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 542 removed outlier: 4.027A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 551 removed outlier: 3.675A pdb=" N GLN J 550 " --> pdb=" O GLY J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 removed outlier: 3.527A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR J 586 " --> pdb=" O ALA J 582 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 592 " --> pdb=" O GLU J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 659 removed outlier: 3.503A pdb=" N ASP J 659 " --> pdb=" O ILE J 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 117 removed outlier: 4.104A pdb=" N GLU K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 126 Processing helix chain 'K' and resid 179 through 181 No H-bonds generated for 'chain 'K' and resid 179 through 181' Processing helix chain 'K' and resid 193 through 198 removed outlier: 3.978A pdb=" N ASN K 197 " --> pdb=" O ILE K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 353 removed outlier: 3.761A pdb=" N GLU K 351 " --> pdb=" O GLY K 347 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS K 352 " --> pdb=" O LYS K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 459B through 463 Processing helix chain 'K' and resid 476 through 484 removed outlier: 3.562A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU K 482 " --> pdb=" O ASN K 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.894A pdb=" N ASP M 31 " --> pdb=" O ASN M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 removed outlier: 4.169A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.937A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.592A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 120 through 121 removed outlier: 3.958A pdb=" N VAL G 120 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA7, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 312 removed outlier: 6.204A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 322 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 10 through 11 current: chain 'S' and resid 45 through 52 removed outlier: 3.668A pdb=" N GLN S 56 " --> pdb=" O ASN S 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 56 through 58 current: chain 'S' and resid 100B through 103 Processing sheet with id=AB2, first strand: chain 'U' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'U' and resid 53 through 54 removed outlier: 5.723A pdb=" N LEU U 46 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN U 37 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.614A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 68 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.247A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.887A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.524A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.991A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.243A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC7, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.554A pdb=" N LEU D 82 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 11 current: chain 'D' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 58 current: chain 'D' and resid 100B through 103 Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.842A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.599A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.787A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.617A pdb=" N TRP F 35 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.557A pdb=" N GLU I 81 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR I 68 " --> pdb=" O GLU I 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.178A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 603 through 609 removed outlier: 7.934A pdb=" N CYS J 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N TYR K 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR J 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL K 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL J 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AD9, first strand: chain 'K' and resid 75 through 76 removed outlier: 3.709A pdb=" N VAL K 75 " --> pdb=" O CYS K 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'K' and resid 120 through 121 removed outlier: 3.902A pdb=" N VAL K 120 " --> pdb=" O GLN K 203 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 130 through 133 Processing sheet with id=AE4, first strand: chain 'K' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 261 current: chain 'K' and resid 284 through 312 removed outlier: 6.192A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN K 315 " --> pdb=" O ILE K 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 315 through 322 current: chain 'K' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 381 through 385 current: chain 'K' and resid 465 through 470 Processing sheet with id=AE5, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 11 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 58 current: chain 'M' and resid 100B through 103 Processing sheet with id=AE7, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AE8, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.892A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.561A pdb=" N VAL O 19 " --> pdb=" O ILE O 75 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.832A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP O 35 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.584A pdb=" N SER P 25 " --> pdb=" O TYR P 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU P 81 " --> pdb=" O THR P 68 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR P 68 " --> pdb=" O GLU P 81 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.160A pdb=" N GLU P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1827 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: 10.75 Time building geometry restraints manager: 10.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8224 1.34 - 1.46: 7627 1.46 - 1.59: 12066 1.59 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 28103 Sorted by residual: bond pdb=" C ARG G 166 " pdb=" N ASP G 167 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.39e-02 5.18e+03 5.73e+00 bond pdb=" O3 PO4 C 601 " pdb=" P PO4 C 601 " ideal model delta sigma weight residual 1.569 1.522 0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" O2 PO4 C 601 " pdb=" P PO4 C 601 " ideal model delta sigma weight residual 1.567 1.523 0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" O4 PO4 C 601 " pdb=" P PO4 C 601 " ideal model delta sigma weight residual 1.568 1.524 0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C ARG G 166 " pdb=" O ARG G 166 " ideal model delta sigma weight residual 1.236 1.209 0.028 1.26e-02 6.30e+03 4.81e+00 ... (remaining 28098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 36227 1.42 - 2.84: 1491 2.84 - 4.26: 287 4.26 - 5.68: 144 5.68 - 7.10: 82 Bond angle restraints: 38231 Sorted by residual: angle pdb=" CA CYS K 247 " pdb=" CB CYS K 247 " pdb=" SG CYS K 247 " ideal model delta sigma weight residual 114.40 121.50 -7.10 2.30e+00 1.89e-01 9.53e+00 angle pdb=" N ALA F 51 " pdb=" CA ALA F 51 " pdb=" CB ALA F 51 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.07e+00 angle pdb=" N ARG G 166 " pdb=" CA ARG G 166 " pdb=" CB ARG G 166 " ideal model delta sigma weight residual 110.28 114.76 -4.48 1.55e+00 4.16e-01 8.36e+00 angle pdb=" C SER I 2 " pdb=" N TYR I 3 " pdb=" CA TYR I 3 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.92e+00 angle pdb=" N ILE O 29 " pdb=" CA ILE O 29 " pdb=" C ILE O 29 " ideal model delta sigma weight residual 111.90 109.79 2.11 8.10e-01 1.52e+00 6.76e+00 ... (remaining 38226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 18023 24.23 - 48.47: 731 48.47 - 72.70: 207 72.70 - 96.93: 133 96.93 - 121.16: 64 Dihedral angle restraints: 19158 sinusoidal: 10038 harmonic: 9120 Sorted by residual: dihedral pdb=" CD ARG G 166 " pdb=" NE ARG G 166 " pdb=" CZ ARG G 166 " pdb=" NH1 ARG G 166 " ideal model delta sinusoidal sigma weight residual 0.00 -85.93 85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS K 218 " pdb=" SG CYS K 218 " pdb=" SG CYS K 247 " pdb=" CB CYS K 247 " ideal model delta sinusoidal sigma weight residual 93.00 32.76 60.24 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -142.38 56.38 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 19155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3978 0.058 - 0.116: 640 0.116 - 0.174: 164 0.174 - 0.232: 4 0.232 - 0.290: 18 Chirality restraints: 4804 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C5 BMA 3 3 " pdb=" C4 BMA 3 3 " pdb=" C6 BMA 3 3 " pdb=" O5 BMA 3 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C5 BMA p 3 " pdb=" C4 BMA p 3 " pdb=" C6 BMA p 3 " pdb=" O5 BMA p 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 4801 not shown) Planarity restraints: 4673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 166 " 1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG G 166 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 166 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG G 166 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 166 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 252 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO K 253 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 99 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO F 100 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 100 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 100 " 0.020 5.00e-02 4.00e+02 ... (remaining 4670 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 194 2.52 - 3.11: 21121 3.11 - 3.71: 38176 3.71 - 4.30: 59276 4.30 - 4.90: 99590 Nonbonded interactions: 218357 Sorted by model distance: nonbonded pdb=" OG1 THR B 606 " pdb=" O VAL G 36 " model vdw 1.922 3.040 nonbonded pdb=" OG1 THR A 606 " pdb=" O VAL C 36 " model vdw 1.974 3.040 nonbonded pdb=" OG1 THR U 22 " pdb=" OE2 GLU U 70 " model vdw 2.047 3.040 nonbonded pdb=" OE2 GLU S 23 " pdb=" OG1 THR S 75 " model vdw 2.081 3.040 nonbonded pdb=" O GLN P 1 " pdb=" OG SER P 2 " model vdw 2.133 3.040 ... (remaining 218352 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 '0' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain 'R' selection = chain 'T' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '1' selection = chain 'Z' selection = chain 'n' } ncs_group { reference = (chain '3' and resid 1 through 6) selection = (chain 'Q' and resid 1 through 6) selection = (chain 'X' and resid 1 through 6) selection = (chain 'b' and resid 1 through 6) selection = (chain 'g' and resid 1 through 6) selection = (chain 'l' and resid 1 through 6) selection = (chain 'p' and resid 1 through 6) selection = (chain 'u' and resid 1 through 6) selection = (chain 'z' and resid 1 through 6) } ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 517 through 661 or resid 701 through 702)) selection = chain 'J' } ncs_group { reference = (chain 'C' and (resid 31 through 506 or resid 602 through 608)) selection = (chain 'G' and (resid 31 through 506 or resid 602 through 608)) selection = (chain 'K' and (resid 31 through 506 or resid 602 through 608)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'V' selection = chain 'j' selection = chain 'x' } ncs_group { reference = chain 'W' selection = chain 'k' selection = chain 'y' } 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: 7.990 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 65.720 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.300 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.005 0.047 28345 Z= 0.254 Angle : 0.785 9.235 38909 Z= 0.338 Chirality : 0.050 0.290 4804 Planarity : 0.008 0.496 4598 Dihedral : 16.748 121.165 13158 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.02 % Rotamer: Outliers : 0.22 % Allowed : 0.58 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3111 helix: -0.18 (0.29), residues: 360 sheet: 0.45 (0.17), residues: 1023 loop : -0.85 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 631 HIS 0.005 0.001 HIS H 96 PHE 0.008 0.001 PHE G 383 TYR 0.007 0.001 TYR N 49 ARG 0.004 0.000 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 75) link_NAG-ASN : angle 1.87344 ( 225) link_ALPHA1-6 : bond 0.00349 ( 27) link_ALPHA1-6 : angle 1.82793 ( 81) link_BETA1-4 : bond 0.00386 ( 59) link_BETA1-4 : angle 1.43916 ( 177) link_ALPHA1-2 : bond 0.00161 ( 6) link_ALPHA1-2 : angle 2.18201 ( 18) link_ALPHA1-3 : bond 0.00419 ( 24) link_ALPHA1-3 : angle 2.10735 ( 72) hydrogen bonds : bond 0.25999 ( 710) hydrogen bonds : angle 8.79486 ( 1827) link_BETA1-6 : bond 0.00553 ( 3) link_BETA1-6 : angle 1.44094 ( 9) SS BOND : bond 0.00337 ( 48) SS BOND : angle 1.03793 ( 96) covalent geometry : bond 0.00538 (28103) covalent geometry : angle 0.75874 (38231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 433 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 405 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7332 (p0) REVERT: G 464 ASP cc_start: 0.7291 (m-30) cc_final: 0.6864 (m-30) REVERT: S 98 ASP cc_start: 0.8528 (m-30) cc_final: 0.8012 (t0) REVERT: A 601 LYS cc_start: 0.8781 (mttp) cc_final: 0.8527 (mttm) REVERT: C 396 ILE cc_start: 0.7953 (tp) cc_final: 0.7718 (tp) REVERT: D 23 GLU cc_start: 0.7732 (tt0) cc_final: 0.7503 (tt0) REVERT: D 98 ASP cc_start: 0.8436 (m-30) cc_final: 0.8056 (t0) REVERT: F 79 GLN cc_start: 0.7728 (mt0) cc_final: 0.7385 (tm-30) REVERT: F 82 ASP cc_start: 0.8061 (t0) cc_final: 0.7712 (t0) REVERT: K 100 MET cc_start: 0.9147 (mtp) cc_final: 0.8916 (mtm) REVERT: K 397 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7471 (t0) REVERT: N 77 ASN cc_start: 0.7276 (t0) cc_final: 0.6910 (t0) REVERT: N 79 GLN cc_start: 0.7206 (mm110) cc_final: 0.6998 (mm110) outliers start: 6 outliers final: 3 residues processed: 439 average time/residue: 1.4489 time to fit residues: 732.7445 Evaluate side-chains 294 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain G residue 474 ASN Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 405 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 79 optimal weight: 0.0270 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN G 67 ASN G 146 ASN G 183 GLN S 46 GLN L 6 GLN H 56 HIS H 96 HIS H 99 GLN C 67 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 64 GLN E 3 GLN E 26 ASN I 105 GLN K 258 GLN M 6 GLN M 39 GLN N 26 ASN N 38 GLN P 96 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077132 restraints weight = 46610.991| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.17 r_work: 0.2930 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28345 Z= 0.133 Angle : 0.652 11.142 38909 Z= 0.313 Chirality : 0.047 0.356 4804 Planarity : 0.004 0.042 4598 Dihedral : 13.598 106.717 7333 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 2.06 % Allowed : 9.01 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 3111 helix: 0.90 (0.29), residues: 342 sheet: 0.58 (0.17), residues: 993 loop : -0.73 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 50 HIS 0.002 0.001 HIS G 249 PHE 0.009 0.001 PHE F 71 TYR 0.012 0.001 TYR N 36 ARG 0.007 0.001 ARG H 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 75) link_NAG-ASN : angle 1.80169 ( 225) link_ALPHA1-6 : bond 0.00555 ( 27) link_ALPHA1-6 : angle 1.81374 ( 81) link_BETA1-4 : bond 0.00471 ( 59) link_BETA1-4 : angle 1.71936 ( 177) link_ALPHA1-2 : bond 0.00507 ( 6) link_ALPHA1-2 : angle 1.88519 ( 18) link_ALPHA1-3 : bond 0.00949 ( 24) link_ALPHA1-3 : angle 2.93736 ( 72) hydrogen bonds : bond 0.05440 ( 710) hydrogen bonds : angle 5.90861 ( 1827) link_BETA1-6 : bond 0.00635 ( 3) link_BETA1-6 : angle 1.01671 ( 9) SS BOND : bond 0.00440 ( 48) SS BOND : angle 1.17383 ( 96) covalent geometry : bond 0.00299 (28103) covalent geometry : angle 0.60954 (38231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 2.843 Fit side-chains REVERT: G 102 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: G 164 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: G 186 ASN cc_start: 0.7890 (t0) cc_final: 0.7679 (t0) REVERT: G 373 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8330 (mmm) REVERT: G 464 ASP cc_start: 0.7379 (m-30) cc_final: 0.6874 (m-30) REVERT: U 40 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.7994 (tpp-160) REVERT: U 77 ASN cc_start: 0.6602 (t0) cc_final: 0.6184 (t0) REVERT: U 79 GLN cc_start: 0.6336 (mm110) cc_final: 0.6032 (mm110) REVERT: A 601 LYS cc_start: 0.8360 (mttp) cc_final: 0.8005 (mttm) REVERT: C 186 ASN cc_start: 0.7941 (t0) cc_final: 0.7714 (t0) REVERT: C 428 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7082 (mm-40) REVERT: D 23 GLU cc_start: 0.7398 (tt0) cc_final: 0.7076 (tt0) REVERT: D 98 ASP cc_start: 0.8420 (m-30) cc_final: 0.7807 (t0) REVERT: E 77 ASN cc_start: 0.6684 (t0) cc_final: 0.6081 (t0) REVERT: E 79 GLN cc_start: 0.6084 (mm110) cc_final: 0.5725 (mm110) REVERT: E 96 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: F 11 LEU cc_start: 0.8152 (mm) cc_final: 0.7855 (mp) REVERT: F 61 ARG cc_start: 0.6097 (ptt90) cc_final: 0.5710 (ptt90) REVERT: F 70 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7312 (mtp85) REVERT: I 48 MET cc_start: 0.7598 (mtp) cc_final: 0.7325 (mtp) REVERT: J 584 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7536 (mt-10) REVERT: K 100 MET cc_start: 0.8687 (mtp) cc_final: 0.8336 (mtm) REVERT: K 186 ASN cc_start: 0.7913 (t0) cc_final: 0.7674 (t0) REVERT: K 397 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7710 (t0) REVERT: N 3 GLN cc_start: 0.7293 (mm-40) cc_final: 0.7040 (mm-40) REVERT: N 77 ASN cc_start: 0.6793 (t0) cc_final: 0.6359 (t0) REVERT: N 79 GLN cc_start: 0.6375 (mm110) cc_final: 0.6142 (mm110) REVERT: O 27 GLN cc_start: 0.7600 (tm-30) cc_final: 0.6719 (tm-30) REVERT: O 28 ASP cc_start: 0.7879 (t70) cc_final: 0.7530 (t70) REVERT: O 79 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: P 3 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6893 (t80) outliers start: 57 outliers final: 23 residues processed: 357 average time/residue: 1.4525 time to fit residues: 600.8277 Evaluate side-chains 317 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 80 MET Chi-restraints excluded: chain P residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 74 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN G 146 ASN U 79 GLN H 82BASN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN C 428 GLN D 6 GLN E 26 ASN E 37 GLN E 79 GLN I 105 GLN K 61 HIS K 67 ASN K 146 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 ASN P 96 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.111131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074971 restraints weight = 46987.363| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.15 r_work: 0.2885 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28345 Z= 0.217 Angle : 0.702 13.064 38909 Z= 0.334 Chirality : 0.049 0.347 4804 Planarity : 0.004 0.043 4598 Dihedral : 12.346 98.717 7325 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.92 % Rotamer: Outliers : 3.40 % Allowed : 10.10 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3111 helix: 0.90 (0.29), residues: 342 sheet: 0.41 (0.17), residues: 993 loop : -0.87 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 50 HIS 0.004 0.001 HIS K 66 PHE 0.014 0.001 PHE G 383 TYR 0.014 0.001 TYR E 49 ARG 0.008 0.001 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 75) link_NAG-ASN : angle 2.15518 ( 225) link_ALPHA1-6 : bond 0.00494 ( 27) link_ALPHA1-6 : angle 1.81890 ( 81) link_BETA1-4 : bond 0.00451 ( 59) link_BETA1-4 : angle 1.74208 ( 177) link_ALPHA1-2 : bond 0.00449 ( 6) link_ALPHA1-2 : angle 1.94460 ( 18) link_ALPHA1-3 : bond 0.00954 ( 24) link_ALPHA1-3 : angle 2.71140 ( 72) hydrogen bonds : bond 0.05123 ( 710) hydrogen bonds : angle 5.43348 ( 1827) link_BETA1-6 : bond 0.00585 ( 3) link_BETA1-6 : angle 1.12150 ( 9) SS BOND : bond 0.00568 ( 48) SS BOND : angle 1.49599 ( 96) covalent geometry : bond 0.00535 (28103) covalent geometry : angle 0.65726 (38231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 306 time to evaluate : 2.802 Fit side-chains REVERT: G 102 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: G 186 ASN cc_start: 0.8156 (t0) cc_final: 0.7933 (t0) REVERT: G 428 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7315 (mm-40) REVERT: G 464 ASP cc_start: 0.7390 (m-30) cc_final: 0.6900 (m-30) REVERT: U 26 ASN cc_start: 0.7773 (t0) cc_final: 0.7395 (t0) REVERT: U 40 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8174 (tpp-160) REVERT: U 69 GLN cc_start: 0.7180 (mm110) cc_final: 0.6874 (mm110) REVERT: U 77 ASN cc_start: 0.6648 (t0) cc_final: 0.6191 (t0) REVERT: U 79 GLN cc_start: 0.6372 (mm-40) cc_final: 0.5967 (mm110) REVERT: H 3 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6688 (m-80) REVERT: A 601 LYS cc_start: 0.8394 (mttp) cc_final: 0.7945 (mttm) REVERT: C 80 ASN cc_start: 0.8352 (t0) cc_final: 0.8142 (t0) REVERT: C 164 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: C 186 ASN cc_start: 0.8275 (t0) cc_final: 0.8045 (t0) REVERT: D 23 GLU cc_start: 0.7563 (tt0) cc_final: 0.7152 (tt0) REVERT: D 86 ASP cc_start: 0.8812 (m-30) cc_final: 0.8580 (m-30) REVERT: D 98 ASP cc_start: 0.8464 (m-30) cc_final: 0.7806 (t0) REVERT: D 100 ASP cc_start: 0.8301 (m-30) cc_final: 0.8021 (p0) REVERT: E 77 ASN cc_start: 0.6993 (t0) cc_final: 0.6363 (t0) REVERT: E 79 GLN cc_start: 0.6379 (mm-40) cc_final: 0.5915 (mm110) REVERT: E 96 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: F 11 LEU cc_start: 0.8157 (mm) cc_final: 0.7894 (mp) REVERT: F 70 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7582 (mtp85) REVERT: F 82 ASP cc_start: 0.7745 (t0) cc_final: 0.7544 (t0) REVERT: I 26 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8049 (mtp85) REVERT: I 72 ASP cc_start: 0.7353 (t0) cc_final: 0.6999 (t70) REVERT: J 584 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7543 (mt-10) REVERT: J 654 ASP cc_start: 0.8188 (m-30) cc_final: 0.7794 (m-30) REVERT: K 100 MET cc_start: 0.8720 (mtp) cc_final: 0.8393 (mtm) REVERT: K 102 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: K 186 ASN cc_start: 0.8024 (t0) cc_final: 0.7817 (t0) REVERT: K 397 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7804 (t0) REVERT: N 3 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6770 (mm-40) REVERT: N 77 ASN cc_start: 0.6874 (t0) cc_final: 0.6414 (t0) REVERT: N 79 GLN cc_start: 0.6202 (mm110) cc_final: 0.5953 (mm110) REVERT: O 27 GLN cc_start: 0.7702 (tm-30) cc_final: 0.6694 (tm-30) REVERT: O 79 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: P 3 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6836 (t80) outliers start: 94 outliers final: 42 residues processed: 366 average time/residue: 1.3442 time to fit residues: 573.7146 Evaluate side-chains 348 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 428 GLN Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 475 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 74 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 175 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS C 143 ASN C 146 ASN C 183 GLN D 6 GLN D 28 ASN D 39 GLN E 3 GLN E 26 ASN E 38 GLN I 105 GLN K 146 ASN M 39 GLN N 26 ASN P 96 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.112159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076039 restraints weight = 47119.810| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.17 r_work: 0.2911 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28345 Z= 0.149 Angle : 0.648 10.927 38909 Z= 0.308 Chirality : 0.047 0.351 4804 Planarity : 0.004 0.043 4598 Dihedral : 11.567 92.726 7325 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 2.61 % Allowed : 12.16 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3111 helix: 1.21 (0.29), residues: 342 sheet: 0.52 (0.17), residues: 978 loop : -0.84 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 50 HIS 0.002 0.001 HIS K 66 PHE 0.010 0.001 PHE G 383 TYR 0.012 0.001 TYR L 3 ARG 0.009 0.001 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 75) link_NAG-ASN : angle 1.95101 ( 225) link_ALPHA1-6 : bond 0.00593 ( 27) link_ALPHA1-6 : angle 1.76368 ( 81) link_BETA1-4 : bond 0.00406 ( 59) link_BETA1-4 : angle 1.57353 ( 177) link_ALPHA1-2 : bond 0.00417 ( 6) link_ALPHA1-2 : angle 1.79477 ( 18) link_ALPHA1-3 : bond 0.01043 ( 24) link_ALPHA1-3 : angle 2.76307 ( 72) hydrogen bonds : bond 0.04325 ( 710) hydrogen bonds : angle 5.16574 ( 1827) link_BETA1-6 : bond 0.00605 ( 3) link_BETA1-6 : angle 1.07481 ( 9) SS BOND : bond 0.00509 ( 48) SS BOND : angle 1.17177 ( 96) covalent geometry : bond 0.00353 (28103) covalent geometry : angle 0.60553 (38231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 2.762 Fit side-chains REVERT: G 102 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: G 186 ASN cc_start: 0.8196 (t0) cc_final: 0.7950 (t0) REVERT: G 464 ASP cc_start: 0.7388 (m-30) cc_final: 0.6892 (m-30) REVERT: S 86 ASP cc_start: 0.8748 (m-30) cc_final: 0.8347 (m-30) REVERT: U 26 ASN cc_start: 0.7743 (t0) cc_final: 0.7421 (t0) REVERT: U 40 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8145 (tpp-160) REVERT: U 77 ASN cc_start: 0.6925 (t0) cc_final: 0.6478 (t0) REVERT: U 79 GLN cc_start: 0.6315 (mm-40) cc_final: 0.5902 (mm110) REVERT: H 3 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: C 80 ASN cc_start: 0.8363 (t0) cc_final: 0.8149 (t0) REVERT: C 164 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: C 186 ASN cc_start: 0.8341 (t0) cc_final: 0.8068 (t0) REVERT: C 396 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7532 (tp) REVERT: C 397 ASN cc_start: 0.7410 (t0) cc_final: 0.7119 (m-40) REVERT: D 23 GLU cc_start: 0.7509 (tt0) cc_final: 0.7096 (tt0) REVERT: D 86 ASP cc_start: 0.8717 (m-30) cc_final: 0.8363 (m-30) REVERT: D 98 ASP cc_start: 0.8459 (m-30) cc_final: 0.7794 (t0) REVERT: D 100 ASP cc_start: 0.8233 (m-30) cc_final: 0.8017 (p0) REVERT: E 77 ASN cc_start: 0.7192 (t0) cc_final: 0.6610 (t0) REVERT: E 79 GLN cc_start: 0.6427 (mm-40) cc_final: 0.5968 (mm110) REVERT: E 87 PHE cc_start: 0.6320 (m-10) cc_final: 0.6099 (m-10) REVERT: E 96 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: F 61 ARG cc_start: 0.6130 (ptt90) cc_final: 0.5892 (ptt90) REVERT: I 26 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7844 (mtp85) REVERT: I 72 ASP cc_start: 0.7308 (t0) cc_final: 0.6756 (t0) REVERT: J 584 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7523 (mt-10) REVERT: K 100 MET cc_start: 0.8652 (mtp) cc_final: 0.8362 (mtm) REVERT: K 102 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: K 186 ASN cc_start: 0.8080 (t0) cc_final: 0.7843 (t0) REVERT: K 397 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7914 (t0) REVERT: K 475 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8100 (tp) REVERT: M 74 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8664 (m-30) REVERT: M 100 ASP cc_start: 0.7891 (m-30) cc_final: 0.7447 (OUTLIER) REVERT: N 3 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6690 (mm-40) REVERT: N 40 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7764 (tpp-160) REVERT: N 61 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7401 (ttm170) REVERT: N 77 ASN cc_start: 0.6851 (t0) cc_final: 0.6527 (t0) REVERT: N 79 GLN cc_start: 0.6230 (mm110) cc_final: 0.5932 (mm110) REVERT: O 27 GLN cc_start: 0.7717 (tm-30) cc_final: 0.6762 (tm-30) REVERT: O 79 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: O 82 ASP cc_start: 0.7425 (m-30) cc_final: 0.7185 (m-30) REVERT: O 92 LYS cc_start: 0.8474 (ptmm) cc_final: 0.8258 (ptmm) REVERT: P 3 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6821 (t80) outliers start: 72 outliers final: 39 residues processed: 355 average time/residue: 1.4004 time to fit residues: 579.5829 Evaluate side-chains 338 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 475 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 6 GLN D 28 ASN E 26 ASN I 105 GLN K 146 ASN M 39 GLN N 26 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077270 restraints weight = 46823.047| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.16 r_work: 0.2933 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28345 Z= 0.122 Angle : 0.618 9.433 38909 Z= 0.291 Chirality : 0.046 0.346 4804 Planarity : 0.004 0.041 4598 Dihedral : 10.814 90.246 7325 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 2.79 % Allowed : 12.67 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3111 helix: 1.54 (0.29), residues: 342 sheet: 0.59 (0.17), residues: 1005 loop : -0.76 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 50 HIS 0.002 0.000 HIS J 564 PHE 0.008 0.001 PHE F 94 TYR 0.011 0.001 TYR U 71 ARG 0.009 0.001 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 75) link_NAG-ASN : angle 1.79082 ( 225) link_ALPHA1-6 : bond 0.00646 ( 27) link_ALPHA1-6 : angle 1.74473 ( 81) link_BETA1-4 : bond 0.00425 ( 59) link_BETA1-4 : angle 1.44580 ( 177) link_ALPHA1-2 : bond 0.00417 ( 6) link_ALPHA1-2 : angle 1.72374 ( 18) link_ALPHA1-3 : bond 0.01094 ( 24) link_ALPHA1-3 : angle 2.72388 ( 72) hydrogen bonds : bond 0.03864 ( 710) hydrogen bonds : angle 4.89992 ( 1827) link_BETA1-6 : bond 0.00618 ( 3) link_BETA1-6 : angle 1.06084 ( 9) SS BOND : bond 0.00443 ( 48) SS BOND : angle 0.98882 ( 96) covalent geometry : bond 0.00280 (28103) covalent geometry : angle 0.57973 (38231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 314 time to evaluate : 2.850 Fit side-chains REVERT: G 102 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: G 164 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: G 186 ASN cc_start: 0.8168 (t0) cc_final: 0.7901 (t0) REVERT: G 464 ASP cc_start: 0.7381 (m-30) cc_final: 0.6883 (m-30) REVERT: S 5 LEU cc_start: 0.7565 (mp) cc_final: 0.7288 (mt) REVERT: S 86 ASP cc_start: 0.8751 (m-30) cc_final: 0.8369 (m-30) REVERT: S 100 ASP cc_start: 0.7960 (m-30) cc_final: 0.7518 (p0) REVERT: U 26 ASN cc_start: 0.7682 (t0) cc_final: 0.7394 (t0) REVERT: U 77 ASN cc_start: 0.7090 (t0) cc_final: 0.6694 (t0) REVERT: U 79 GLN cc_start: 0.6338 (mm-40) cc_final: 0.5987 (mm110) REVERT: H 3 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: A 530 MET cc_start: 0.7755 (mtt) cc_final: 0.7233 (mtt) REVERT: C 80 ASN cc_start: 0.8392 (t0) cc_final: 0.8137 (t0) REVERT: C 164 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: C 186 ASN cc_start: 0.8292 (t0) cc_final: 0.8063 (t0) REVERT: D 23 GLU cc_start: 0.7537 (tt0) cc_final: 0.7110 (tt0) REVERT: D 83 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6371 (mtp180) REVERT: D 86 ASP cc_start: 0.8612 (m-30) cc_final: 0.8184 (m-30) REVERT: D 98 ASP cc_start: 0.8414 (m-30) cc_final: 0.7786 (t0) REVERT: E 77 ASN cc_start: 0.7312 (t0) cc_final: 0.6764 (t0) REVERT: E 79 GLN cc_start: 0.6172 (mm-40) cc_final: 0.5770 (mm110) REVERT: E 96 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: F 27 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7621 (tm-30) REVERT: I 26 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7808 (mtp85) REVERT: I 72 ASP cc_start: 0.7250 (t0) cc_final: 0.6695 (t70) REVERT: J 584 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7512 (mt-10) REVERT: K 100 MET cc_start: 0.8601 (mtp) cc_final: 0.8338 (mtm) REVERT: K 102 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8107 (mm-30) REVERT: K 186 ASN cc_start: 0.8169 (t0) cc_final: 0.7921 (t0) REVERT: K 397 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7954 (t0) REVERT: M 28 ASN cc_start: 0.8129 (p0) cc_final: 0.7396 (p0) REVERT: M 74 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8649 (m-30) REVERT: M 86 ASP cc_start: 0.8617 (m-30) cc_final: 0.8146 (m-30) REVERT: N 3 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6717 (mm-40) REVERT: N 61 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7335 (ttm170) REVERT: N 77 ASN cc_start: 0.6972 (t0) cc_final: 0.6659 (t0) REVERT: N 79 GLN cc_start: 0.6285 (mm110) cc_final: 0.5976 (mm110) REVERT: O 27 GLN cc_start: 0.7803 (tm-30) cc_final: 0.6865 (tm-30) REVERT: O 79 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: P 3 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6722 (t80) REVERT: P 26 ARG cc_start: 0.7465 (mtm110) cc_final: 0.7118 (mtp-110) outliers start: 77 outliers final: 45 residues processed: 363 average time/residue: 1.3619 time to fit residues: 573.3474 Evaluate side-chains 354 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 55 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS A 575 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 6 GLN D 28 ASN E 3 GLN E 26 ASN I 105 GLN K 146 ASN M 39 GLN N 26 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.113214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077322 restraints weight = 46940.135| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.16 r_work: 0.2936 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28345 Z= 0.128 Angle : 0.624 9.049 38909 Z= 0.293 Chirality : 0.046 0.348 4804 Planarity : 0.004 0.041 4598 Dihedral : 10.335 87.324 7325 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 2.68 % Allowed : 13.64 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3111 helix: 1.68 (0.29), residues: 342 sheet: 0.62 (0.17), residues: 987 loop : -0.72 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 50 HIS 0.001 0.001 HIS J 564 PHE 0.008 0.001 PHE K 383 TYR 0.016 0.001 TYR L 3 ARG 0.010 0.001 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 75) link_NAG-ASN : angle 1.81184 ( 225) link_ALPHA1-6 : bond 0.00659 ( 27) link_ALPHA1-6 : angle 1.73923 ( 81) link_BETA1-4 : bond 0.00423 ( 59) link_BETA1-4 : angle 1.43380 ( 177) link_ALPHA1-2 : bond 0.00392 ( 6) link_ALPHA1-2 : angle 1.72996 ( 18) link_ALPHA1-3 : bond 0.01120 ( 24) link_ALPHA1-3 : angle 2.69262 ( 72) hydrogen bonds : bond 0.03770 ( 710) hydrogen bonds : angle 4.77065 ( 1827) link_BETA1-6 : bond 0.00611 ( 3) link_BETA1-6 : angle 1.06747 ( 9) SS BOND : bond 0.00425 ( 48) SS BOND : angle 1.00456 ( 96) covalent geometry : bond 0.00297 (28103) covalent geometry : angle 0.58612 (38231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 306 time to evaluate : 3.028 Fit side-chains revert: symmetry clash REVERT: G 102 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: G 164 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: G 186 ASN cc_start: 0.8081 (t0) cc_final: 0.7787 (t0) REVERT: G 464 ASP cc_start: 0.7382 (m-30) cc_final: 0.6886 (m-30) REVERT: S 5 LEU cc_start: 0.7589 (mp) cc_final: 0.7293 (mt) REVERT: S 86 ASP cc_start: 0.8716 (m-30) cc_final: 0.8208 (m-30) REVERT: S 100 ASP cc_start: 0.7937 (m-30) cc_final: 0.7582 (p0) REVERT: U 26 ASN cc_start: 0.7683 (t0) cc_final: 0.7472 (t0) REVERT: U 40 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8045 (tpp-160) REVERT: U 77 ASN cc_start: 0.7112 (t0) cc_final: 0.6641 (t0) REVERT: U 79 GLN cc_start: 0.6333 (mm-40) cc_final: 0.5831 (mm110) REVERT: L 70 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7306 (mmm-85) REVERT: H 3 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6681 (m-80) REVERT: A 530 MET cc_start: 0.7805 (mtt) cc_final: 0.7413 (mtt) REVERT: A 657 GLU cc_start: 0.8214 (tt0) cc_final: 0.7806 (tt0) REVERT: C 80 ASN cc_start: 0.8407 (t0) cc_final: 0.8149 (t0) REVERT: C 164 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: C 186 ASN cc_start: 0.8305 (t0) cc_final: 0.8005 (t0) REVERT: D 23 GLU cc_start: 0.7546 (tt0) cc_final: 0.7107 (tt0) REVERT: D 82 LEU cc_start: 0.7786 (mp) cc_final: 0.7571 (mp) REVERT: D 83 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6389 (mtp180) REVERT: D 86 ASP cc_start: 0.8557 (m-30) cc_final: 0.8202 (m-30) REVERT: D 98 ASP cc_start: 0.8402 (m-30) cc_final: 0.7836 (t0) REVERT: E 77 ASN cc_start: 0.7316 (t0) cc_final: 0.6773 (t0) REVERT: E 79 GLN cc_start: 0.6166 (mm-40) cc_final: 0.5764 (mm110) REVERT: F 11 LEU cc_start: 0.7810 (mm) cc_final: 0.7470 (mp) REVERT: I 26 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7814 (mtp85) REVERT: I 82 ASN cc_start: 0.6576 (t0) cc_final: 0.6273 (t0) REVERT: K 100 MET cc_start: 0.8582 (mtp) cc_final: 0.8376 (mtm) REVERT: K 102 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: K 186 ASN cc_start: 0.8149 (t0) cc_final: 0.7888 (t0) REVERT: K 397 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7908 (t0) REVERT: M 28 ASN cc_start: 0.7983 (p0) cc_final: 0.7367 (p0) REVERT: M 74 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: N 3 GLN cc_start: 0.7371 (mm-40) cc_final: 0.6691 (mm-40) REVERT: N 61 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7336 (ttm170) REVERT: N 77 ASN cc_start: 0.7026 (t0) cc_final: 0.6728 (t0) REVERT: N 79 GLN cc_start: 0.6188 (mm110) cc_final: 0.5865 (mm110) REVERT: O 27 GLN cc_start: 0.7869 (tm-30) cc_final: 0.6890 (tm-30) REVERT: O 70 ARG cc_start: 0.7435 (mtp85) cc_final: 0.7084 (mtm110) REVERT: O 79 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: P 3 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6686 (t80) REVERT: P 26 ARG cc_start: 0.7445 (mtm110) cc_final: 0.7086 (mtp-110) outliers start: 74 outliers final: 41 residues processed: 349 average time/residue: 1.3804 time to fit residues: 559.9039 Evaluate side-chains 348 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 98 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 86 optimal weight: 0.2980 chunk 246 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 295 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN G 258 GLN S 28 ASN H 96 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 28 ASN E 26 ASN I 105 GLN K 146 ASN M 39 GLN N 26 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075145 restraints weight = 47107.685| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.16 r_work: 0.2892 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28345 Z= 0.212 Angle : 0.687 10.281 38909 Z= 0.324 Chirality : 0.048 0.353 4804 Planarity : 0.004 0.042 4598 Dihedral : 10.312 83.080 7325 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.64 % Rotamer: Outliers : 2.71 % Allowed : 13.97 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3111 helix: 1.38 (0.29), residues: 342 sheet: 0.44 (0.16), residues: 1050 loop : -0.83 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 50 HIS 0.003 0.001 HIS G 375 PHE 0.014 0.001 PHE G 383 TYR 0.015 0.001 TYR N 49 ARG 0.010 0.001 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 75) link_NAG-ASN : angle 2.08911 ( 225) link_ALPHA1-6 : bond 0.00594 ( 27) link_ALPHA1-6 : angle 1.77624 ( 81) link_BETA1-4 : bond 0.00428 ( 59) link_BETA1-4 : angle 1.59324 ( 177) link_ALPHA1-2 : bond 0.00389 ( 6) link_ALPHA1-2 : angle 1.87162 ( 18) link_ALPHA1-3 : bond 0.01067 ( 24) link_ALPHA1-3 : angle 2.71145 ( 72) hydrogen bonds : bond 0.04402 ( 710) hydrogen bonds : angle 4.87743 ( 1827) link_BETA1-6 : bond 0.00583 ( 3) link_BETA1-6 : angle 1.10998 ( 9) SS BOND : bond 0.00550 ( 48) SS BOND : angle 1.26833 ( 96) covalent geometry : bond 0.00523 (28103) covalent geometry : angle 0.64528 (38231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 3.072 Fit side-chains REVERT: G 102 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: G 186 ASN cc_start: 0.8174 (t0) cc_final: 0.7902 (t0) REVERT: G 464 ASP cc_start: 0.7413 (m-30) cc_final: 0.6930 (m-30) REVERT: S 5 LEU cc_start: 0.7603 (mp) cc_final: 0.7325 (mt) REVERT: S 86 ASP cc_start: 0.8754 (m-30) cc_final: 0.8355 (m-30) REVERT: U 26 ASN cc_start: 0.7756 (t0) cc_final: 0.7493 (t0) REVERT: U 77 ASN cc_start: 0.7141 (t0) cc_final: 0.6708 (t0) REVERT: U 79 GLN cc_start: 0.6290 (mm-40) cc_final: 0.5869 (mm110) REVERT: L 70 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7357 (mmm-85) REVERT: C 80 ASN cc_start: 0.8421 (t0) cc_final: 0.8156 (t0) REVERT: C 164 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: C 186 ASN cc_start: 0.8318 (t0) cc_final: 0.8032 (t0) REVERT: D 23 GLU cc_start: 0.7633 (tt0) cc_final: 0.7308 (tt0) REVERT: D 82 LEU cc_start: 0.7758 (mp) cc_final: 0.7486 (mp) REVERT: D 83 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6370 (mtp180) REVERT: D 86 ASP cc_start: 0.8631 (m-30) cc_final: 0.8259 (m-30) REVERT: D 98 ASP cc_start: 0.8458 (m-30) cc_final: 0.7827 (t0) REVERT: E 77 ASN cc_start: 0.7344 (t0) cc_final: 0.6792 (t0) REVERT: E 79 GLN cc_start: 0.6417 (mm-40) cc_final: 0.5997 (mm110) REVERT: E 96 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7911 (pm20) REVERT: F 11 LEU cc_start: 0.7810 (mm) cc_final: 0.7601 (mp) REVERT: I 26 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7895 (mtp85) REVERT: I 72 ASP cc_start: 0.7302 (t0) cc_final: 0.6865 (t70) REVERT: I 82 ASN cc_start: 0.6497 (t0) cc_final: 0.6245 (t0) REVERT: J 584 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7409 (mt-10) REVERT: K 100 MET cc_start: 0.8611 (mtp) cc_final: 0.8398 (mtm) REVERT: K 102 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: K 186 ASN cc_start: 0.8133 (t0) cc_final: 0.7877 (t0) REVERT: K 397 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7961 (t0) REVERT: M 13 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7622 (mttm) REVERT: M 74 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: M 100 ASP cc_start: 0.8558 (p0) cc_final: 0.8261 (p0) REVERT: N 3 GLN cc_start: 0.7435 (mm-40) cc_final: 0.6717 (mm-40) REVERT: N 26 ASN cc_start: 0.7678 (t0) cc_final: 0.7113 (t0) REVERT: N 61 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7376 (ttm170) REVERT: N 77 ASN cc_start: 0.7010 (t0) cc_final: 0.6719 (t0) REVERT: N 79 GLN cc_start: 0.6165 (mm110) cc_final: 0.5846 (mm110) REVERT: O 27 GLN cc_start: 0.7903 (tm-30) cc_final: 0.6912 (tm-30) REVERT: O 79 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: P 3 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6757 (t80) REVERT: P 26 ARG cc_start: 0.7449 (mtm110) cc_final: 0.7069 (mtp-110) outliers start: 75 outliers final: 41 residues processed: 347 average time/residue: 1.3560 time to fit residues: 548.1973 Evaluate side-chains 348 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 151 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN G 146 ASN S 28 ASN S 39 GLN U 38 GLN H 96 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 28 ASN E 3 GLN E 26 ASN E 37 GLN I 105 GLN K 146 ASN M 39 GLN N 79 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074423 restraints weight = 47064.305| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.16 r_work: 0.2880 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28345 Z= 0.231 Angle : 0.712 11.155 38909 Z= 0.336 Chirality : 0.049 0.354 4804 Planarity : 0.004 0.041 4598 Dihedral : 10.226 76.210 7325 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.17 % Favored : 92.74 % Rotamer: Outliers : 2.82 % Allowed : 14.08 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3111 helix: 1.19 (0.29), residues: 342 sheet: 0.31 (0.16), residues: 1050 loop : -0.93 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 50 HIS 0.003 0.001 HIS G 375 PHE 0.015 0.001 PHE G 383 TYR 0.019 0.001 TYR L 3 ARG 0.010 0.001 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 75) link_NAG-ASN : angle 2.24854 ( 225) link_ALPHA1-6 : bond 0.00582 ( 27) link_ALPHA1-6 : angle 1.77705 ( 81) link_BETA1-4 : bond 0.00432 ( 59) link_BETA1-4 : angle 1.67225 ( 177) link_ALPHA1-2 : bond 0.00421 ( 6) link_ALPHA1-2 : angle 1.93692 ( 18) link_ALPHA1-3 : bond 0.01087 ( 24) link_ALPHA1-3 : angle 2.73179 ( 72) hydrogen bonds : bond 0.04611 ( 710) hydrogen bonds : angle 4.96260 ( 1827) link_BETA1-6 : bond 0.00574 ( 3) link_BETA1-6 : angle 1.10043 ( 9) SS BOND : bond 0.00554 ( 48) SS BOND : angle 1.32443 ( 96) covalent geometry : bond 0.00572 (28103) covalent geometry : angle 0.66775 (38231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 2.825 Fit side-chains revert: symmetry clash REVERT: G 102 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8107 (mm-30) REVERT: G 164 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: G 464 ASP cc_start: 0.7427 (m-30) cc_final: 0.6941 (m-30) REVERT: S 100 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7572 (p0) REVERT: U 26 ASN cc_start: 0.7665 (t0) cc_final: 0.7416 (t0) REVERT: U 40 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8022 (tpp-160) REVERT: U 77 ASN cc_start: 0.7109 (t0) cc_final: 0.6718 (t0) REVERT: U 79 GLN cc_start: 0.6253 (mm-40) cc_final: 0.5871 (mm110) REVERT: L 70 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7371 (mtp85) REVERT: H 3 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: C 80 ASN cc_start: 0.8444 (t0) cc_final: 0.8187 (t0) REVERT: C 100 MET cc_start: 0.8382 (mtp) cc_final: 0.8056 (mtt) REVERT: C 164 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: C 186 ASN cc_start: 0.8308 (t0) cc_final: 0.8077 (t0) REVERT: D 23 GLU cc_start: 0.7694 (tt0) cc_final: 0.7272 (tt0) REVERT: D 83 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6387 (mtp180) REVERT: D 86 ASP cc_start: 0.8650 (m-30) cc_final: 0.8257 (m-30) REVERT: D 98 ASP cc_start: 0.8449 (m-30) cc_final: 0.7768 (t0) REVERT: E 26 ASN cc_start: 0.8138 (t0) cc_final: 0.7886 (t0) REVERT: E 77 ASN cc_start: 0.7380 (t0) cc_final: 0.6833 (t0) REVERT: E 79 GLN cc_start: 0.6330 (mm-40) cc_final: 0.5953 (mm110) REVERT: E 81 GLU cc_start: 0.7320 (pm20) cc_final: 0.7071 (pm20) REVERT: I 72 ASP cc_start: 0.7391 (t0) cc_final: 0.6965 (t70) REVERT: I 74 ASP cc_start: 0.7968 (p0) cc_final: 0.7758 (p0) REVERT: I 82 ASN cc_start: 0.6652 (t0) cc_final: 0.6417 (t0) REVERT: K 102 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: K 186 ASN cc_start: 0.8135 (t0) cc_final: 0.7895 (t0) REVERT: K 397 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7958 (t0) REVERT: M 13 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7564 (mttt) REVERT: M 28 ASN cc_start: 0.8030 (p0) cc_final: 0.7320 (p0) REVERT: M 31 ASP cc_start: 0.8618 (m-30) cc_final: 0.7973 (m-30) REVERT: M 74 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8663 (m-30) REVERT: N 3 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6684 (mm-40) REVERT: N 26 ASN cc_start: 0.7811 (t0) cc_final: 0.7246 (t0) REVERT: N 61 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7307 (ttm170) REVERT: N 65 ARG cc_start: 0.6546 (ptm160) cc_final: 0.6254 (ptm160) REVERT: N 77 ASN cc_start: 0.6989 (t0) cc_final: 0.6718 (t0) REVERT: O 70 ARG cc_start: 0.7417 (mtp85) cc_final: 0.7053 (mtm110) REVERT: O 79 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: P 3 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6823 (t80) REVERT: P 26 ARG cc_start: 0.7438 (mtm110) cc_final: 0.7048 (mtp-110) outliers start: 78 outliers final: 42 residues processed: 349 average time/residue: 1.3506 time to fit residues: 548.6784 Evaluate side-chains 350 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 100 ASP Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 135 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 188 optimal weight: 0.0980 chunk 269 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 199 optimal weight: 0.0770 chunk 41 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN S 39 GLN H 96 HIS A 577 GLN C 146 ASN C 183 GLN C 258 GLN D 6 GLN E 37 GLN I 105 GLN K 146 ASN M 39 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077540 restraints weight = 47013.069| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.17 r_work: 0.2933 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28345 Z= 0.118 Angle : 0.628 8.501 38909 Z= 0.297 Chirality : 0.046 0.352 4804 Planarity : 0.004 0.040 4598 Dihedral : 9.544 71.637 7325 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 1.85 % Allowed : 15.38 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3111 helix: 1.65 (0.29), residues: 342 sheet: 0.47 (0.16), residues: 1014 loop : -0.82 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 50 HIS 0.002 0.000 HIS M 35 PHE 0.009 0.001 PHE J 651 TYR 0.012 0.001 TYR U 71 ARG 0.010 0.001 ARG N 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 75) link_NAG-ASN : angle 1.77870 ( 225) link_ALPHA1-6 : bond 0.00718 ( 27) link_ALPHA1-6 : angle 1.68499 ( 81) link_BETA1-4 : bond 0.00439 ( 59) link_BETA1-4 : angle 1.39145 ( 177) link_ALPHA1-2 : bond 0.00434 ( 6) link_ALPHA1-2 : angle 1.69533 ( 18) link_ALPHA1-3 : bond 0.01223 ( 24) link_ALPHA1-3 : angle 2.64311 ( 72) hydrogen bonds : bond 0.03602 ( 710) hydrogen bonds : angle 4.69062 ( 1827) link_BETA1-6 : bond 0.00624 ( 3) link_BETA1-6 : angle 1.07390 ( 9) SS BOND : bond 0.00422 ( 48) SS BOND : angle 0.93599 ( 96) covalent geometry : bond 0.00267 (28103) covalent geometry : angle 0.59228 (38231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 2.906 Fit side-chains revert: symmetry clash REVERT: G 102 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: G 464 ASP cc_start: 0.7388 (m-30) cc_final: 0.6904 (m-30) REVERT: S 5 LEU cc_start: 0.7620 (mp) cc_final: 0.7317 (mt) REVERT: S 86 ASP cc_start: 0.8615 (m-30) cc_final: 0.8170 (m-30) REVERT: U 40 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8051 (tpp-160) REVERT: U 70 GLU cc_start: 0.7546 (tt0) cc_final: 0.7143 (tt0) REVERT: U 77 ASN cc_start: 0.7089 (t0) cc_final: 0.6701 (t0) REVERT: U 79 GLN cc_start: 0.6346 (mm-40) cc_final: 0.5888 (mm110) REVERT: H 3 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: A 530 MET cc_start: 0.7553 (mtt) cc_final: 0.6903 (mtt) REVERT: A 657 GLU cc_start: 0.8175 (tt0) cc_final: 0.7761 (tt0) REVERT: C 186 ASN cc_start: 0.8298 (t0) cc_final: 0.8082 (t0) REVERT: C 322 ILE cc_start: 0.8107 (mt) cc_final: 0.7904 (mt) REVERT: D 5 LEU cc_start: 0.7786 (mp) cc_final: 0.7547 (mt) REVERT: D 23 GLU cc_start: 0.7602 (tt0) cc_final: 0.7195 (tt0) REVERT: D 83 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6360 (mtp180) REVERT: D 86 ASP cc_start: 0.8426 (m-30) cc_final: 0.8044 (m-30) REVERT: D 98 ASP cc_start: 0.8436 (m-30) cc_final: 0.7829 (t0) REVERT: E 26 ASN cc_start: 0.8087 (t0) cc_final: 0.7835 (t0) REVERT: E 77 ASN cc_start: 0.7361 (t0) cc_final: 0.6825 (t0) REVERT: E 79 GLN cc_start: 0.6191 (mm-40) cc_final: 0.5785 (mm110) REVERT: F 70 ARG cc_start: 0.7480 (mtp-110) cc_final: 0.7173 (mtp85) REVERT: I 3 TYR cc_start: 0.7363 (m-80) cc_final: 0.7137 (m-80) REVERT: I 26 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7825 (mtm110) REVERT: I 72 ASP cc_start: 0.7446 (t0) cc_final: 0.7002 (t70) REVERT: I 82 ASN cc_start: 0.6637 (t0) cc_final: 0.6394 (t0) REVERT: K 102 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: K 186 ASN cc_start: 0.8124 (t0) cc_final: 0.7885 (t0) REVERT: K 397 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7902 (t0) REVERT: M 28 ASN cc_start: 0.7935 (p0) cc_final: 0.7224 (p0) REVERT: M 31 ASP cc_start: 0.8657 (m-30) cc_final: 0.8008 (m-30) REVERT: N 3 GLN cc_start: 0.7441 (mm-40) cc_final: 0.6678 (mm-40) REVERT: N 61 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7317 (ttm170) REVERT: N 77 ASN cc_start: 0.7167 (t0) cc_final: 0.6854 (t0) REVERT: N 79 GLN cc_start: 0.6095 (mm-40) cc_final: 0.5672 (mm110) REVERT: O 70 ARG cc_start: 0.7396 (mtp85) cc_final: 0.7060 (mtm110) REVERT: O 79 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: O 82 ASP cc_start: 0.7661 (m-30) cc_final: 0.7404 (m-30) REVERT: P 3 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6706 (t80) REVERT: P 26 ARG cc_start: 0.7413 (mtm110) cc_final: 0.7037 (mtp-110) REVERT: P 66 ARG cc_start: 0.6072 (mtp180) cc_final: 0.5505 (ttp-170) outliers start: 51 outliers final: 30 residues processed: 342 average time/residue: 1.4653 time to fit residues: 587.7745 Evaluate side-chains 333 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 232 optimal weight: 0.0470 chunk 183 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN G 146 ASN S 28 ASN S 39 GLN H 96 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 146 ASN C 183 GLN D 6 GLN D 28 ASN E 3 GLN I 105 GLN K 146 ASN M 39 GLN N 26 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077573 restraints weight = 46703.596| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.15 r_work: 0.2934 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28345 Z= 0.129 Angle : 0.636 8.651 38909 Z= 0.301 Chirality : 0.046 0.350 4804 Planarity : 0.004 0.042 4598 Dihedral : 9.370 71.450 7325 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 1.66 % Allowed : 15.85 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3111 helix: 1.72 (0.29), residues: 342 sheet: 0.51 (0.16), residues: 1014 loop : -0.79 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 571 HIS 0.002 0.001 HIS G 375 PHE 0.009 0.001 PHE J 651 TYR 0.024 0.001 TYR G 173 ARG 0.010 0.001 ARG N 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 75) link_NAG-ASN : angle 1.83461 ( 225) link_ALPHA1-6 : bond 0.00701 ( 27) link_ALPHA1-6 : angle 1.68983 ( 81) link_BETA1-4 : bond 0.00437 ( 59) link_BETA1-4 : angle 1.41898 ( 177) link_ALPHA1-2 : bond 0.00369 ( 6) link_ALPHA1-2 : angle 1.74441 ( 18) link_ALPHA1-3 : bond 0.01197 ( 24) link_ALPHA1-3 : angle 2.67422 ( 72) hydrogen bonds : bond 0.03651 ( 710) hydrogen bonds : angle 4.63903 ( 1827) link_BETA1-6 : bond 0.00606 ( 3) link_BETA1-6 : angle 1.06417 ( 9) SS BOND : bond 0.00501 ( 48) SS BOND : angle 1.04926 ( 96) covalent geometry : bond 0.00299 (28103) covalent geometry : angle 0.59849 (38231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 299 time to evaluate : 3.199 Fit side-chains revert: symmetry clash REVERT: G 102 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: G 464 ASP cc_start: 0.7391 (m-30) cc_final: 0.6908 (m-30) REVERT: S 5 LEU cc_start: 0.7607 (mp) cc_final: 0.7296 (mt) REVERT: S 83 ARG cc_start: 0.6954 (mpp80) cc_final: 0.6691 (mpp80) REVERT: S 86 ASP cc_start: 0.8620 (m-30) cc_final: 0.8165 (m-30) REVERT: S 98 ASP cc_start: 0.8488 (m-30) cc_final: 0.7615 (t0) REVERT: U 40 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8067 (tpp-160) REVERT: U 70 GLU cc_start: 0.7522 (tt0) cc_final: 0.7124 (tt0) REVERT: U 77 ASN cc_start: 0.7079 (t0) cc_final: 0.6695 (t0) REVERT: U 79 GLN cc_start: 0.6299 (mm-40) cc_final: 0.5859 (mm110) REVERT: L 27 GLN cc_start: 0.7471 (tm-30) cc_final: 0.6528 (tm-30) REVERT: L 70 ARG cc_start: 0.7607 (mmm160) cc_final: 0.7230 (mmm-85) REVERT: H 3 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: A 530 MET cc_start: 0.7678 (mtt) cc_final: 0.7059 (mtt) REVERT: A 657 GLU cc_start: 0.8177 (tt0) cc_final: 0.7835 (tt0) REVERT: C 106 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7167 (mt-10) REVERT: C 186 ASN cc_start: 0.8332 (t0) cc_final: 0.8112 (t0) REVERT: D 5 LEU cc_start: 0.7810 (mp) cc_final: 0.7555 (mt) REVERT: D 23 GLU cc_start: 0.7657 (tt0) cc_final: 0.7252 (tt0) REVERT: D 83 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6392 (mtp180) REVERT: D 86 ASP cc_start: 0.8439 (m-30) cc_final: 0.8033 (m-30) REVERT: D 98 ASP cc_start: 0.8426 (m-30) cc_final: 0.7826 (t0) REVERT: E 26 ASN cc_start: 0.8106 (t0) cc_final: 0.7836 (t0) REVERT: E 77 ASN cc_start: 0.7392 (t0) cc_final: 0.7001 (t0) REVERT: E 96 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: F 70 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7337 (mtp85) REVERT: I 72 ASP cc_start: 0.7456 (t0) cc_final: 0.7069 (t70) REVERT: I 82 ASN cc_start: 0.6650 (t0) cc_final: 0.6435 (t0) REVERT: K 102 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: K 186 ASN cc_start: 0.8102 (t0) cc_final: 0.7864 (t0) REVERT: K 397 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7961 (t0) REVERT: M 28 ASN cc_start: 0.7867 (p0) cc_final: 0.7192 (p0) REVERT: N 3 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6730 (mm-40) REVERT: N 26 ASN cc_start: 0.7693 (t0) cc_final: 0.7337 (t0) REVERT: N 61 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7334 (ttm170) REVERT: N 77 ASN cc_start: 0.7171 (t0) cc_final: 0.6894 (t0) REVERT: N 79 GLN cc_start: 0.6106 (mm-40) cc_final: 0.5714 (mm110) REVERT: O 70 ARG cc_start: 0.7424 (mtp85) cc_final: 0.7055 (mtm110) REVERT: O 79 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: P 3 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6709 (t80) REVERT: P 26 ARG cc_start: 0.7344 (mtm110) cc_final: 0.6956 (mtp-110) REVERT: P 66 ARG cc_start: 0.6018 (mtp180) cc_final: 0.5517 (ttp-170) outliers start: 46 outliers final: 31 residues processed: 326 average time/residue: 1.3653 time to fit residues: 516.1384 Evaluate side-chains 332 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 40 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 194 optimal weight: 0.0000 chunk 294 optimal weight: 0.9980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN S 39 GLN H 96 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 6 GLN D 28 ASN E 79 GLN K 146 ASN M 39 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077229 restraints weight = 46932.586| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.15 r_work: 0.2933 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 28345 Z= 0.151 Angle : 0.758 59.198 38909 Z= 0.390 Chirality : 0.046 0.350 4804 Planarity : 0.004 0.040 4598 Dihedral : 9.370 71.443 7325 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 1.81 % Allowed : 15.89 % Favored : 82.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3111 helix: 1.73 (0.29), residues: 342 sheet: 0.51 (0.16), residues: 1014 loop : -0.79 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 571 HIS 0.002 0.000 HIS G 375 PHE 0.008 0.001 PHE G 383 TYR 0.014 0.001 TYR G 173 ARG 0.010 0.000 ARG I 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 75) link_NAG-ASN : angle 1.83463 ( 225) link_ALPHA1-6 : bond 0.00701 ( 27) link_ALPHA1-6 : angle 1.68986 ( 81) link_BETA1-4 : bond 0.00436 ( 59) link_BETA1-4 : angle 1.41850 ( 177) link_ALPHA1-2 : bond 0.00368 ( 6) link_ALPHA1-2 : angle 1.74420 ( 18) link_ALPHA1-3 : bond 0.01198 ( 24) link_ALPHA1-3 : angle 2.67534 ( 72) hydrogen bonds : bond 0.03649 ( 710) hydrogen bonds : angle 4.63831 ( 1827) link_BETA1-6 : bond 0.00606 ( 3) link_BETA1-6 : angle 1.06394 ( 9) SS BOND : bond 0.00462 ( 48) SS BOND : angle 1.02945 ( 96) covalent geometry : bond 0.00339 (28103) covalent geometry : angle 0.72916 (38231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16656.62 seconds wall clock time: 289 minutes 18.49 seconds (17358.49 seconds total)