Starting phenix.real_space_refine on Mon Jun 23 09:30:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pc2_13316/06_2025/7pc2_13316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pc2_13316/06_2025/7pc2_13316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pc2_13316/06_2025/7pc2_13316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pc2_13316/06_2025/7pc2_13316.map" model { file = "/net/cci-nas-00/data/ceres_data/7pc2_13316/06_2025/7pc2_13316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pc2_13316/06_2025/7pc2_13316.cif" } resolution = 2.8 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= 0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 16839 2.51 5 N 4398 2.21 5 O 5670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27063 Number of models: 1 Model: "" Number of chains: 68 Chain: "O" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "P" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "R" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 Chain: "C" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "D" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "K" 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: "G" 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: "I" 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: "L" 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: "H" 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: "J" 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: "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: 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: 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: 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 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: 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: "f" 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 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: "l" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "m" 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: "n" 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: "o" 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: "p" 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: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "r" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "s" 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: "t" 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: "u" 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: "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: 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "0" 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: "1" 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: "2" 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: "3" 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "6" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "7" 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: "8" 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: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 Time building chain proxies: 17.43, per 1000 atoms: 0.64 Number of scatterers: 27063 At special positions: 0 Unit cell: (182.75, 173.4, 123.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 5670 8.00 N 4398 7.00 C 16839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 105 " - pdb=" SG CYS O 110 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 105 " - pdb=" SG CYS Q 110 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=1.74 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.36 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.42 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.72 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=1.94 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.94 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 218 " - pdb=" SG CYS C 247 " distance=2.56 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 C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 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 5 5 " - " MAN 5 6 " " MAN 5 7 " - " MAN 5 8 " " MAN 6 4 " - " MAN 6 5 " " MAN 6 5 " - " MAN 6 6 " " MAN 6 8 " - " MAN 6 9 " " MAN 6 10 " - " MAN 6 11 " " MAN W 5 " - " MAN W 6 " " MAN W 8 " - " MAN W 9 " " MAN X 4 " - " MAN X 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN a 10 " - " MAN a 11 " " MAN b 5 " - " MAN b 6 " " MAN l 4 " - " MAN l 5 " " MAN q 5 " - " MAN q 6 " " MAN q 7 " - " MAN q 8 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " " MAN r 10 " - " MAN r 11 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " " MAN y 5 " - " MAN y 6 " " MAN y 8 " - " MAN y 9 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 5 3 " - " MAN 5 7 " " MAN 5 4 " - " MAN 5 5 " " BMA 6 3 " - " MAN 6 4 " " MAN 6 7 " - " MAN 6 8 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 7 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 7 " " MAN b 4 " - " MAN b 5 " " BMA e 3 " - " MAN e 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 7 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 8 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 7 " " BMA y 3 " - " MAN y 8 " " MAN y 4 " - " MAN y 7 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 5 3 " - " MAN 5 4 " " BMA 6 3 " - " MAN 6 7 " " MAN 6 7 " - " MAN 6 10 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 5 " " BMA l 3 " - " MAN l 6 " " MAN l 6 " - " MAN l 8 " " BMA n 3 " - " MAN n 5 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 10 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " " BMA y 3 " - " MAN y 4 " " MAN y 4 " - " MAN y 5 " " BMA z 3 " - " MAN z 6 " " MAN z 6 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " 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 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " 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 y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN C 301 " " NAG 1 1 " - " ASN C 363 " " NAG 2 1 " - " ASN C 386 " " NAG 3 1 " - " ASN C 392 " " NAG 4 1 " - " ASN C 448 " " NAG 5 1 " - " ASN C 295 " " NAG 6 1 " - " ASN C 332 " " NAG 7 1 " - " ASN L 72 " " NAG 8 1 " - " ASN H 72 " " NAG 9 1 " - " ASN J 72 " " NAG A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 355 " " NAG A 603 " - " ASN A 411 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 234 " " NAG B 601 " - " ASN B 234 " " NAG B 602 " - " ASN B 355 " " NAG B 603 " - " ASN B 339 " " NAG B 604 " - " ASN B 411 " " NAG B 605 " - " ASN B 137 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 411 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 133 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 160 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 301 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 332 " " NAG b 1 " - " ASN A 295 " " NAG c 1 " - " ASN A 392 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN B 88 " " NAG h 1 " - " ASN B 133 " " NAG i 1 " - " ASN B 156 " " NAG j 1 " - " ASN B 160 " " NAG k 1 " - " ASN B 197 " " NAG l 1 " - " ASN B 276 " " NAG m 1 " - " ASN B 301 " " NAG n 1 " - " ASN B 363 " " NAG o 1 " - " ASN B 386 " " NAG p 1 " - " ASN B 448 " " NAG q 1 " - " ASN B 295 " " NAG r 1 " - " ASN B 332 " " NAG s 1 " - " ASN B 262 " " NAG t 1 " - " ASN B 392 " " NAG u 1 " - " ASN C 88 " " NAG v 1 " - " ASN C 156 " " NAG w 1 " - " ASN C 160 " " NAG x 1 " - " ASN C 197 " " NAG y 1 " - " ASN C 262 " " NAG z 1 " - " ASN C 276 " Time building additional restraints: 10.15 Conformation dependent library (CDL) restraints added in 4.9 seconds 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5700 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 57 sheets defined 15.4% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'O' and resid 111 through 116 removed outlier: 3.568A pdb=" N TYR O 116 " --> pdb=" O TRP O 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.813A pdb=" N PHE P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 116 removed outlier: 3.548A pdb=" N TYR M 116 " --> pdb=" O TRP M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 116 removed outlier: 3.533A pdb=" N TYR Q 116 " --> pdb=" O TRP Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.848A pdb=" N PHE R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.235A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.587A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.567A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.695A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.596A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.214A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.523A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 352 removed outlier: 3.584A pdb=" N VAL B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.634A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.615A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.721A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.576A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.578A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.904A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.660A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 634 removed outlier: 3.819A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.546A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.601A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.011A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.933A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 581 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 627 through 634 removed outlier: 3.823A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.508A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.836A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 659 " --> pdb=" O LYS E 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.906A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.970A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 634 removed outlier: 3.677A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.612A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 663 removed outlier: 3.612A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.687A pdb=" N TYR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 removed outlier: 3.674A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.549A pdb=" N ASP G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.709A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.750A pdb=" N TYR I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.065A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.834A pdb=" N SER P 7 " --> pdb=" O SER P 22 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER P 67 " --> pdb=" O GLU P 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.584A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'M' and resid 58 through 60 removed outlier: 5.093A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N SER N 7 " --> pdb=" O SER N 22 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER N 67 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.523A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN N 92 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG N 96 " --> pdb=" O ASN N 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.523A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.157A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.657A pdb=" N SER R 7 " --> pdb=" O SER R 22 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER R 22 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 67 " --> pdb=" O GLU R 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.558A pdb=" N LEU R 11 " --> pdb=" O GLU R 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.292A pdb=" N VAL D 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL A 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR D 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TYR A 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N CYS D 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.872A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.668A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AB9, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AC1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC2, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.447A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.004A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.633A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AC6, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.245A pdb=" N VAL F 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL B 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR F 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR B 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N CYS F 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.881A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.728A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 130 through 133 Processing sheet with id=AD2, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'B' and resid 259 through 261 removed outlier: 5.965A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.730A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.233A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.863A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.730A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AE1, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.994A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.609A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.518A pdb=" N THR K 110 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.518A pdb=" N THR K 110 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.567A pdb=" N THR G 110 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.567A pdb=" N THR G 110 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 18 through 24 Processing sheet with id=AF3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.571A pdb=" N THR I 110 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.571A pdb=" N THR I 110 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.542A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.771A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.728A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 45 through 48 removed outlier: 6.787A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.636A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 799 hydrogen bonds defined for protein. 2007 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: 14.60 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 23853 1.52 - 1.89: 3753 1.89 - 2.25: 0 2.25 - 2.62: 0 2.62 - 2.98: 11 Bond restraints: 27617 Sorted by residual: bond pdb=" C GLY H 27 " pdb=" N TYR H 32 " ideal model delta sigma weight residual 1.330 2.981 -1.651 1.30e-02 5.92e+03 1.61e+04 bond pdb=" C GLY L 27 " pdb=" N TYR L 32 " ideal model delta sigma weight residual 1.330 2.915 -1.585 1.30e-02 5.92e+03 1.49e+04 bond pdb=" C TYR L 91 " pdb=" N GLU L 96 " ideal model delta sigma weight residual 1.332 2.895 -1.563 1.29e-02 6.01e+03 1.47e+04 bond pdb=" C ASP C 141 " pdb=" N MET C 150 " ideal model delta sigma weight residual 1.333 2.930 -1.597 1.36e-02 5.41e+03 1.38e+04 bond pdb=" C GLY J 27 " pdb=" N TYR J 32 " ideal model delta sigma weight residual 1.330 2.925 -1.596 1.38e-02 5.25e+03 1.34e+04 ... (remaining 27612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.67: 37478 16.67 - 33.34: 14 33.34 - 50.01: 1 50.01 - 66.68: 1 66.68 - 83.35: 9 Bond angle restraints: 37503 Sorted by residual: angle pdb=" O GLY J 27 " pdb=" C GLY J 27 " pdb=" N TYR J 32 " ideal model delta sigma weight residual 122.60 46.07 76.53 1.07e+00 8.73e-01 5.12e+03 angle pdb=" O GLY H 27 " pdb=" C GLY H 27 " pdb=" N TYR H 32 " ideal model delta sigma weight residual 122.96 41.61 81.35 1.22e+00 6.72e-01 4.45e+03 angle pdb=" O GLY L 27 " pdb=" C GLY L 27 " pdb=" N TYR L 32 " ideal model delta sigma weight residual 122.95 48.05 74.90 1.15e+00 7.56e-01 4.24e+03 angle pdb=" O TYR J 91 " pdb=" C TYR J 91 " pdb=" N GLU J 96 " ideal model delta sigma weight residual 122.59 39.24 83.35 1.33e+00 5.65e-01 3.93e+03 angle pdb=" O TYR H 91 " pdb=" C TYR H 91 " pdb=" N GLU H 96 " ideal model delta sigma weight residual 122.59 45.81 76.78 1.33e+00 5.65e-01 3.33e+03 ... (remaining 37498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 17469 24.61 - 49.22: 1067 49.22 - 73.83: 249 73.83 - 98.44: 175 98.44 - 123.05: 104 Dihedral angle restraints: 19064 sinusoidal: 10176 harmonic: 8888 Sorted by residual: dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 168.04 -75.04 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS Q 105 " pdb=" SG CYS Q 105 " pdb=" SG CYS Q 110 " pdb=" CB CYS Q 110 " ideal model delta sinusoidal sigma weight residual -86.00 -15.12 -70.88 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 22.99 70.01 1 1.00e+01 1.00e-02 6.32e+01 ... (remaining 19061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 4688 0.172 - 0.345: 55 0.345 - 0.517: 5 0.517 - 0.690: 0 0.690 - 0.862: 1 Chirality restraints: 4749 Sorted by residual: chirality pdb=" CA SER H 7 " pdb=" N SER H 7 " pdb=" C SER H 7 " pdb=" CB SER H 7 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 411 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA SER M 108 " pdb=" N SER M 108 " pdb=" C SER M 108 " pdb=" CB SER M 108 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 4746 not shown) Planarity restraints: 4545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 27 " -0.202 2.00e-02 2.50e+03 2.71e-01 7.35e+02 pdb=" C GLY H 27 " 0.448 2.00e-02 2.50e+03 pdb=" O GLY H 27 " -0.229 2.00e-02 2.50e+03 pdb=" N TYR H 32 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 141 " 0.175 2.00e-02 2.50e+03 2.63e-01 6.89e+02 pdb=" C ASP C 141 " -0.414 2.00e-02 2.50e+03 pdb=" O ASP C 141 " 0.269 2.00e-02 2.50e+03 pdb=" N MET C 150 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 91 " 0.169 2.00e-02 2.50e+03 2.50e-01 6.24e+02 pdb=" C TYR L 91 " -0.417 2.00e-02 2.50e+03 pdb=" O TYR L 91 " 0.214 2.00e-02 2.50e+03 pdb=" N GLU L 96 " 0.034 2.00e-02 2.50e+03 ... (remaining 4542 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 120 2.43 - 3.05: 17279 3.05 - 3.66: 35564 3.66 - 4.28: 56675 4.28 - 4.90: 95883 Nonbonded interactions: 205521 Sorted by model distance: nonbonded pdb=" OD1 ASP M 104 " pdb=" N CYS M 105 " model vdw 1.809 3.120 nonbonded pdb=" CA CYS B 218 " pdb=" SG CYS B 247 " model vdw 1.853 3.064 nonbonded pdb=" O SER H 7 " pdb=" OG SER H 7 " model vdw 2.010 3.040 nonbonded pdb=" OD1 ASP M 120 " pdb=" N VAL M 121 " model vdw 2.043 3.120 nonbonded pdb=" O SER Q 108 " pdb=" O6 NAG b 1 " model vdw 2.098 3.040 ... (remaining 205516 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 '3' selection = chain 'Y' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 'o' selection = chain 't' selection = chain 'u' } ncs_group { reference = chain '1' selection = chain 'e' selection = chain 'n' } ncs_group { reference = chain '4' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'p' selection = chain 'v' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain '5' and resid 5 through 8) selection = (chain 'W' and resid 6 through 9) selection = (chain 'X' and resid 5 through 8) selection = (chain 'b' and resid 4 through 7) selection = (chain 'l' and resid 5 through 8) selection = (chain 'q' and resid 5 through 8) selection = (chain 's' and resid 6 through 9) selection = (chain 'y' and resid 6 through 9) selection = (chain 'z' and resid 5 through 8) } ncs_group { reference = chain '6' selection = chain 'a' selection = chain 'r' } ncs_group { reference = (chain 'A' and (resid 32 through 506 or resid 601 through 604)) selection = (chain 'B' and (resid 32 through 506 or resid 601 through 604)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } 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: 4.720 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: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 71.400 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0637 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 : 0.034 1.651 27874 Z= 2.335 Angle : 1.753 83.352 38227 Z= 1.161 Chirality : 0.060 0.862 4749 Planarity : 0.013 0.271 4481 Dihedral : 19.871 123.049 13223 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.49 % Allowed : 19.55 % Favored : 78.96 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.88 % 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: -3.81 (0.13), residues: 3009 helix: -4.00 (0.14), residues: 381 sheet: -1.46 (0.15), residues: 1014 loop : -2.94 (0.13), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 69 HIS 0.004 0.001 HIS C 66 PHE 0.011 0.002 PHE O 27 TYR 0.016 0.001 TYR O 95 ARG 0.005 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.01074 ( 64) link_NAG-ASN : angle 3.03442 ( 192) link_ALPHA1-6 : bond 0.00419 ( 24) link_ALPHA1-6 : angle 1.94271 ( 72) link_BETA1-4 : bond 0.00529 ( 69) link_BETA1-4 : angle 2.50715 ( 207) link_ALPHA1-2 : bond 0.00220 ( 26) link_ALPHA1-2 : angle 2.20964 ( 78) link_ALPHA1-3 : bond 0.00347 ( 27) link_ALPHA1-3 : angle 2.29227 ( 81) hydrogen bonds : bond 0.24173 ( 772) hydrogen bonds : angle 8.14022 ( 2007) SS BOND : bond 0.20221 ( 47) SS BOND : angle 10.39840 ( 94) covalent geometry : bond 0.03313 (27617) covalent geometry : angle 1.65859 (37503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 496 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 MET cc_start: 0.5710 (ttp) cc_final: 0.4900 (mtt) REVERT: O 32 PHE cc_start: 0.0281 (m-80) cc_final: 0.0056 (m-10) REVERT: O 70 ILE cc_start: 0.2509 (tt) cc_final: 0.1842 (tp) REVERT: P 69 THR cc_start: 0.6625 (t) cc_final: 0.6255 (m) REVERT: M 79 LEU cc_start: 0.2598 (tp) cc_final: 0.1946 (tp) REVERT: Q 50 TYR cc_start: -0.0101 (t80) cc_final: -0.1012 (t80) REVERT: R 42 GLN cc_start: 0.2794 (tt0) cc_final: 0.2568 (tp40) REVERT: A 100 MET cc_start: 0.0557 (mtp) cc_final: -0.0766 (tpt) REVERT: A 298 ARG cc_start: 0.2990 (tmm-80) cc_final: 0.2539 (tpp-160) REVERT: A 386 ASN cc_start: 0.2834 (t0) cc_final: 0.2611 (m-40) REVERT: A 412 ASP cc_start: 0.2372 (OUTLIER) cc_final: 0.1903 (t0) REVERT: C 109 ILE cc_start: -0.0275 (mt) cc_final: -0.0892 (pt) REVERT: C 286 VAL cc_start: 0.3933 (t) cc_final: 0.3489 (t) REVERT: E 550 GLN cc_start: 0.3175 (OUTLIER) cc_final: 0.2793 (mm110) REVERT: K 6 GLN cc_start: -0.2001 (tt0) cc_final: -0.2316 (pm20) REVERT: G 76 TYR cc_start: 0.2674 (m-80) cc_final: 0.2425 (m-80) REVERT: L 42 LYS cc_start: 0.3382 (mmtm) cc_final: 0.2790 (pptt) outliers start: 40 outliers final: 4 residues processed: 527 average time/residue: 1.2827 time to fit residues: 791.7150 Evaluate side-chains 252 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 246 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain H residue 66 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.0770 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN O 74 ASN O 117 GLN P 42 GLN M 3 GLN M 80 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 79 GLN ** N 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN Q 74 ASN R 42 GLN R 92 ASN A 33 ASN A 67 ASN A 99 ASN A 183 GLN A 185 ASN A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 289 ASN A 293 GLN A 462 ASN B 183 GLN B 185 ASN B 195 ASN B 293 GLN B 377 ASN B 432 GLN C 33 ASN C 72 HIS C 185 ASN C 249 HIS C 280 ASN C 293 GLN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN F 651 ASN F 652 GLN K 3 GLN I 6 GLN H 3 GLN H 6 GLN H 34 ASN J 79 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.125811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096027 restraints weight = 58057.151| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.39 r_work: 0.3404 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1105 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27874 Z= 0.171 Angle : 0.896 13.645 38227 Z= 0.422 Chirality : 0.052 0.780 4749 Planarity : 0.005 0.064 4481 Dihedral : 15.208 108.557 7575 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.29 % Allowed : 21.90 % Favored : 72.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.88 % 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: -2.74 (0.14), residues: 3031 helix: -2.41 (0.21), residues: 405 sheet: -0.82 (0.16), residues: 1044 loop : -2.39 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 94 HIS 0.018 0.002 HIS C 352 PHE 0.036 0.002 PHE A 159 TYR 0.027 0.002 TYR J 32 ARG 0.009 0.001 ARG M 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01007 ( 64) link_NAG-ASN : angle 2.96410 ( 192) link_ALPHA1-6 : bond 0.00874 ( 24) link_ALPHA1-6 : angle 1.95062 ( 72) link_BETA1-4 : bond 0.00827 ( 69) link_BETA1-4 : angle 2.32555 ( 207) link_ALPHA1-2 : bond 0.00624 ( 26) link_ALPHA1-2 : angle 2.12395 ( 78) link_ALPHA1-3 : bond 0.01048 ( 27) link_ALPHA1-3 : angle 1.91160 ( 81) hydrogen bonds : bond 0.05127 ( 772) hydrogen bonds : angle 5.90723 ( 2007) SS BOND : bond 0.00574 ( 47) SS BOND : angle 1.91533 ( 94) covalent geometry : bond 0.00360 (27617) covalent geometry : angle 0.84293 (37503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 297 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 20 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4890 (tt) REVERT: M 79 LEU cc_start: 0.2982 (tp) cc_final: 0.2685 (tp) REVERT: M 81 LEU cc_start: -0.0784 (OUTLIER) cc_final: -0.1135 (tm) REVERT: M 83 MET cc_start: 0.1255 (OUTLIER) cc_final: 0.0604 (tpt) REVERT: M 94 TYR cc_start: 0.5609 (m-80) cc_final: 0.5405 (m-10) REVERT: N 4 MET cc_start: 0.5701 (mpp) cc_final: 0.5273 (mpm) REVERT: N 108 LYS cc_start: -0.5179 (OUTLIER) cc_final: -0.5420 (tttm) REVERT: Q 83 MET cc_start: 0.4210 (pmm) cc_final: 0.2249 (tpt) REVERT: R 42 GLN cc_start: 0.3115 (tt0) cc_final: 0.2732 (tp40) REVERT: A 100 MET cc_start: -0.0178 (mtp) cc_final: -0.0706 (tpt) REVERT: A 166 ARG cc_start: -0.2844 (OUTLIER) cc_final: -0.4502 (tpt90) REVERT: A 205 CYS cc_start: -0.1447 (OUTLIER) cc_final: -0.2221 (t) REVERT: A 341 THR cc_start: 0.0317 (p) cc_final: -0.2042 (m) REVERT: A 426 MET cc_start: 0.0069 (pmm) cc_final: -0.1752 (mpt) REVERT: B 116 LEU cc_start: 0.1137 (mm) cc_final: 0.0853 (mm) REVERT: C 258 GLN cc_start: 0.3031 (OUTLIER) cc_final: 0.2563 (tp40) REVERT: D 537 LEU cc_start: 0.3065 (OUTLIER) cc_final: 0.2268 (tt) REVERT: E 550 GLN cc_start: 0.3053 (OUTLIER) cc_final: 0.2487 (mt0) REVERT: K 6 GLN cc_start: -0.1775 (tt0) cc_final: -0.2341 (pm20) REVERT: K 80 MET cc_start: 0.1018 (ptt) cc_final: 0.0376 (ttm) REVERT: G 51 ILE cc_start: 0.0280 (tt) cc_final: -0.0447 (mm) REVERT: G 82 LEU cc_start: 0.0929 (tp) cc_final: 0.0597 (mm) REVERT: I 100 TRP cc_start: 0.1968 (m100) cc_final: -0.1438 (p90) REVERT: L 42 LYS cc_start: 0.3603 (mmtm) cc_final: 0.3086 (pptt) REVERT: H 45 LYS cc_start: 0.3778 (OUTLIER) cc_final: 0.3403 (ptpp) outliers start: 142 outliers final: 36 residues processed: 402 average time/residue: 1.0289 time to fit residues: 503.5863 Evaluate side-chains 269 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 108 LYS Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 117 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 275 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 HIS N 92 ASN Q 109 HIS R 32 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 302 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 195 ASN B 356 ASN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN E 540 GLN E 651 ASN F 543 ASN G 35 HIS G 59 ASN G 62 GLN I 59 ASN H 3 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.136252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.109690 restraints weight = 60705.708| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.45 r_work: 0.3649 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1989 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 27874 Z= 0.230 Angle : 1.019 23.500 38227 Z= 0.477 Chirality : 0.056 0.555 4749 Planarity : 0.006 0.083 4481 Dihedral : 12.394 102.859 7566 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 6.41 % Allowed : 23.35 % Favored : 70.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3031 helix: -1.56 (0.24), residues: 384 sheet: -0.14 (0.16), residues: 918 loop : -2.14 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 427 HIS 0.019 0.002 HIS O 35 PHE 0.035 0.003 PHE A 159 TYR 0.026 0.003 TYR C 217 ARG 0.013 0.001 ARG Q 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00917 ( 64) link_NAG-ASN : angle 3.88151 ( 192) link_ALPHA1-6 : bond 0.01216 ( 24) link_ALPHA1-6 : angle 2.10201 ( 72) link_BETA1-4 : bond 0.00893 ( 69) link_BETA1-4 : angle 2.53329 ( 207) link_ALPHA1-2 : bond 0.00654 ( 26) link_ALPHA1-2 : angle 2.06009 ( 78) link_ALPHA1-3 : bond 0.01095 ( 27) link_ALPHA1-3 : angle 1.88615 ( 81) hydrogen bonds : bond 0.05089 ( 772) hydrogen bonds : angle 6.05014 ( 2007) SS BOND : bond 0.00618 ( 47) SS BOND : angle 2.03315 ( 94) covalent geometry : bond 0.00501 (27617) covalent geometry : angle 0.95441 (37503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 305 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 19 ARG cc_start: 0.4261 (ptm-80) cc_final: 0.3948 (ptm-80) REVERT: M 3 GLN cc_start: 0.6177 (mp-120) cc_final: 0.4548 (tm-30) REVERT: M 79 LEU cc_start: 0.2772 (OUTLIER) cc_final: 0.2521 (tp) REVERT: M 81 LEU cc_start: -0.0379 (OUTLIER) cc_final: -0.0722 (tm) REVERT: M 83 MET cc_start: 0.1214 (mtt) cc_final: 0.0451 (tpt) REVERT: N 4 MET cc_start: 0.6000 (mpp) cc_final: 0.5469 (mpm) REVERT: N 21 LEU cc_start: 0.5443 (mp) cc_final: 0.5106 (tt) REVERT: Q 95 TYR cc_start: 0.2367 (m-80) cc_final: 0.2115 (m-80) REVERT: R 42 GLN cc_start: 0.3324 (tt0) cc_final: 0.2937 (tp40) REVERT: R 78 VAL cc_start: 0.5498 (OUTLIER) cc_final: 0.5166 (p) REVERT: A 100 MET cc_start: 0.0207 (mtp) cc_final: -0.0448 (tpt) REVERT: A 104 MET cc_start: 0.1403 (mtt) cc_final: 0.0965 (tpt) REVERT: A 113 ASP cc_start: 0.0889 (m-30) cc_final: 0.0595 (m-30) REVERT: A 193 LEU cc_start: 0.1543 (OUTLIER) cc_final: 0.1218 (pt) REVERT: A 247 CYS cc_start: 0.2635 (OUTLIER) cc_final: 0.2267 (p) REVERT: C 258 GLN cc_start: 0.3329 (OUTLIER) cc_final: 0.2115 (tp-100) REVERT: C 276 ASN cc_start: -0.0541 (OUTLIER) cc_final: -0.1316 (p0) REVERT: C 338 TRP cc_start: 0.4963 (t-100) cc_final: 0.3626 (t60) REVERT: C 492 GLU cc_start: 0.1591 (OUTLIER) cc_final: 0.1268 (mm-30) REVERT: D 650 GLN cc_start: -0.0890 (OUTLIER) cc_final: -0.1207 (tt0) REVERT: E 535 MET cc_start: 0.4258 (pmt) cc_final: 0.3477 (mmt) REVERT: E 550 GLN cc_start: 0.3493 (OUTLIER) cc_final: 0.2756 (mt0) REVERT: K 80 MET cc_start: 0.1546 (ptt) cc_final: 0.1345 (ttm) REVERT: G 94 ARG cc_start: 0.3868 (ptm160) cc_final: 0.3582 (ptm160) REVERT: I 100 TRP cc_start: 0.2475 (m-10) cc_final: 0.1827 (m100) REVERT: L 4 MET cc_start: 0.4054 (mtp) cc_final: 0.3276 (mmm) REVERT: L 42 LYS cc_start: 0.3609 (mmtm) cc_final: 0.3212 (pptt) outliers start: 172 outliers final: 61 residues processed: 441 average time/residue: 1.4555 time to fit residues: 780.3546 Evaluate side-chains 318 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 247 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 651 ASN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 62 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 262 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 82 GLN O 109 HIS ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 13 GLN R 32 ASN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 315 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN E 590 GLN F 540 GLN G 3 GLN G 59 ASN I 46 GLN I 62 GLN I 108 GLN J 37 GLN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.155634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.135265 restraints weight = 67517.935| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 3.61 r_work: 0.4043 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3455 moved from start: 0.8844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 27874 Z= 0.340 Angle : 1.254 24.423 38227 Z= 0.607 Chirality : 0.064 0.427 4749 Planarity : 0.009 0.134 4481 Dihedral : 11.763 97.535 7566 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.05 % Favored : 91.88 % Rotamer: Outliers : 7.41 % Allowed : 24.99 % Favored : 67.60 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3031 helix: -1.99 (0.23), residues: 381 sheet: -0.46 (0.17), residues: 849 loop : -2.34 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP F 623 HIS 0.014 0.003 HIS B 85 PHE 0.048 0.005 PHE B 176 TYR 0.052 0.004 TYR C 217 ARG 0.014 0.001 ARG A 419 Details of bonding type rmsd link_NAG-ASN : bond 0.01080 ( 64) link_NAG-ASN : angle 3.58743 ( 192) link_ALPHA1-6 : bond 0.01082 ( 24) link_ALPHA1-6 : angle 2.11563 ( 72) link_BETA1-4 : bond 0.00756 ( 69) link_BETA1-4 : angle 2.46440 ( 207) link_ALPHA1-2 : bond 0.00654 ( 26) link_ALPHA1-2 : angle 2.12223 ( 78) link_ALPHA1-3 : bond 0.01122 ( 27) link_ALPHA1-3 : angle 2.11878 ( 81) hydrogen bonds : bond 0.06062 ( 772) hydrogen bonds : angle 7.40871 ( 2007) SS BOND : bond 0.02355 ( 47) SS BOND : angle 2.30228 ( 94) covalent geometry : bond 0.00736 (27617) covalent geometry : angle 1.20941 (37503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 359 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 MET cc_start: 0.6531 (ttt) cc_final: 0.4831 (ttp) REVERT: O 34 MET cc_start: 0.5961 (tpp) cc_final: 0.5749 (tpp) REVERT: O 81 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.4900 (tp) REVERT: O 83 MET cc_start: 0.5440 (ptm) cc_final: 0.5219 (ptm) REVERT: P 2 ILE cc_start: 0.6745 (mm) cc_final: 0.6511 (mm) REVERT: P 104 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6789 (tppt) REVERT: M 51 MET cc_start: 0.1387 (mtm) cc_final: 0.0834 (tpp) REVERT: M 79 LEU cc_start: 0.2127 (tp) cc_final: 0.1510 (tp) REVERT: M 94 TYR cc_start: 0.5022 (OUTLIER) cc_final: 0.3077 (p90) REVERT: N 4 MET cc_start: 0.6378 (mpp) cc_final: 0.5981 (ttt) REVERT: N 21 LEU cc_start: 0.5972 (mp) cc_final: 0.5304 (tt) REVERT: Q 70 ILE cc_start: 0.4201 (OUTLIER) cc_final: 0.3567 (tp) REVERT: Q 101 ILE cc_start: 0.0524 (OUTLIER) cc_final: -0.0003 (pp) REVERT: A 69 TRP cc_start: 0.4186 (OUTLIER) cc_final: 0.3099 (m100) REVERT: A 104 MET cc_start: 0.2898 (mtt) cc_final: 0.1294 (tpt) REVERT: A 178 ARG cc_start: 0.1765 (OUTLIER) cc_final: -0.1066 (pmt170) REVERT: A 247 CYS cc_start: 0.3007 (OUTLIER) cc_final: 0.2467 (p) REVERT: A 305 LYS cc_start: 0.4807 (mtmt) cc_final: 0.4486 (ttpt) REVERT: A 326 ILE cc_start: 0.3992 (OUTLIER) cc_final: 0.3769 (mm) REVERT: A 420 ILE cc_start: 0.5317 (OUTLIER) cc_final: 0.5003 (tt) REVERT: A 434 MET cc_start: 0.1493 (OUTLIER) cc_final: 0.1068 (mmm) REVERT: B 100 MET cc_start: 0.3211 (OUTLIER) cc_final: 0.1554 (mmt) REVERT: B 135 THR cc_start: 0.6516 (t) cc_final: 0.6097 (t) REVERT: B 475 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.4938 (mmt) REVERT: C 340 GLU cc_start: 0.6822 (tt0) cc_final: 0.6561 (mt-10) REVERT: D 591 GLN cc_start: 0.3030 (OUTLIER) cc_final: 0.2367 (mm110) REVERT: D 635 ILE cc_start: 0.2759 (OUTLIER) cc_final: 0.2458 (tp) REVERT: D 650 GLN cc_start: -0.0869 (OUTLIER) cc_final: -0.1223 (tt0) REVERT: K 52 PRO cc_start: 0.5312 (Cg_endo) cc_final: 0.4072 (Cg_exo) REVERT: G 29 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.5284 (mt) REVERT: G 51 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.5117 (pt) REVERT: G 64 GLN cc_start: 0.4143 (mm-40) cc_final: 0.3942 (mm-40) REVERT: L 4 MET cc_start: 0.4025 (mtp) cc_final: 0.3395 (mmm) REVERT: L 42 LYS cc_start: 0.4081 (mmtm) cc_final: 0.3369 (pptt) REVERT: H 77 ASN cc_start: 0.7961 (t0) cc_final: 0.7593 (t0) REVERT: J 67 TRP cc_start: 0.6331 (t60) cc_final: 0.6004 (t60) outliers start: 199 outliers final: 67 residues processed: 510 average time/residue: 1.1120 time to fit residues: 694.1806 Evaluate side-chains 352 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 267 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 262 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 260 optimal weight: 0.1980 chunk 199 optimal weight: 0.1980 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 0.0570 chunk 143 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 257 optimal weight: 0.8980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 GLN Q 1 GLN ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 607 ASN E 650 GLN F 540 GLN I 46 GLN I 62 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.155489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.134551 restraints weight = 66808.271| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.66 r_work: 0.4024 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3410 moved from start: 0.9149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27874 Z= 0.164 Angle : 0.943 19.033 38227 Z= 0.432 Chirality : 0.053 0.855 4749 Planarity : 0.005 0.075 4481 Dihedral : 10.517 92.979 7562 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.77 % Allowed : 29.27 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3031 helix: -0.86 (0.26), residues: 354 sheet: -0.08 (0.17), residues: 897 loop : -2.00 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 395 HIS 0.008 0.001 HIS R 90 PHE 0.033 0.002 PHE J 87 TYR 0.025 0.002 TYR D 643 ARG 0.014 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 64) link_NAG-ASN : angle 3.80873 ( 192) link_ALPHA1-6 : bond 0.00964 ( 24) link_ALPHA1-6 : angle 1.81804 ( 72) link_BETA1-4 : bond 0.00600 ( 69) link_BETA1-4 : angle 2.00563 ( 207) link_ALPHA1-2 : bond 0.00584 ( 26) link_ALPHA1-2 : angle 1.84624 ( 78) link_ALPHA1-3 : bond 0.01152 ( 27) link_ALPHA1-3 : angle 2.07320 ( 81) hydrogen bonds : bond 0.04177 ( 772) hydrogen bonds : angle 6.24862 ( 2007) SS BOND : bond 0.00436 ( 47) SS BOND : angle 1.66758 ( 94) covalent geometry : bond 0.00349 (27617) covalent geometry : angle 0.88373 (37503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 289 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 6 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6117 (pm20) REVERT: O 47 TRP cc_start: 0.6544 (t60) cc_final: 0.6248 (t60) REVERT: O 81 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.4761 (tm) REVERT: O 83 MET cc_start: 0.5171 (ptm) cc_final: 0.4950 (ptm) REVERT: P 2 ILE cc_start: 0.7164 (mm) cc_final: 0.6865 (mt) REVERT: P 18 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7370 (tpp80) REVERT: P 88 CYS cc_start: 0.5149 (OUTLIER) cc_final: 0.4643 (p) REVERT: M 6 GLU cc_start: 0.6114 (mp0) cc_final: 0.2312 (pm20) REVERT: M 18 LEU cc_start: 0.0151 (OUTLIER) cc_final: -0.1121 (pt) REVERT: M 51 MET cc_start: 0.1497 (mtm) cc_final: 0.1051 (tpp) REVERT: M 81 LEU cc_start: 0.1029 (OUTLIER) cc_final: -0.0305 (tm) REVERT: M 83 MET cc_start: 0.0649 (mpt) cc_final: -0.1049 (tpt) REVERT: M 94 TYR cc_start: 0.4796 (OUTLIER) cc_final: 0.2961 (p90) REVERT: M 95 TYR cc_start: 0.1616 (m-80) cc_final: 0.1413 (m-80) REVERT: Q 68 PHE cc_start: 0.4815 (OUTLIER) cc_final: 0.3876 (t80) REVERT: A 100 MET cc_start: 0.0271 (OUTLIER) cc_final: -0.0847 (tpt) REVERT: A 247 CYS cc_start: 0.2745 (OUTLIER) cc_final: 0.1971 (p) REVERT: A 276 ASN cc_start: -0.1407 (OUTLIER) cc_final: -0.2736 (p0) REVERT: A 326 ILE cc_start: 0.3682 (OUTLIER) cc_final: 0.3383 (mm) REVERT: A 434 MET cc_start: 0.0956 (OUTLIER) cc_final: 0.0347 (mmm) REVERT: A 443 ILE cc_start: 0.4516 (OUTLIER) cc_final: 0.4304 (mm) REVERT: B 100 MET cc_start: 0.2981 (pp-130) cc_final: 0.0468 (mmt) REVERT: B 323 ILE cc_start: 0.7409 (tp) cc_final: 0.6872 (pp) REVERT: B 421 LYS cc_start: 0.6392 (mtpp) cc_final: 0.6084 (mtpp) REVERT: B 474 ASP cc_start: 0.5792 (p0) cc_final: 0.5526 (p0) REVERT: B 475 MET cc_start: 0.5720 (mmp) cc_final: 0.5187 (mmt) REVERT: C 166 ARG cc_start: 0.6514 (tmm160) cc_final: 0.5710 (ttt180) REVERT: C 185 GLU cc_start: 0.0771 (OUTLIER) cc_final: 0.0182 (pm20) REVERT: C 275 GLU cc_start: 0.1396 (OUTLIER) cc_final: 0.1012 (pm20) REVERT: D 537 LEU cc_start: 0.3701 (OUTLIER) cc_final: 0.2785 (tt) REVERT: D 591 GLN cc_start: 0.3393 (OUTLIER) cc_final: 0.2818 (mm110) REVERT: D 647 GLU cc_start: 0.5186 (OUTLIER) cc_final: 0.4552 (pt0) REVERT: E 535 MET cc_start: 0.4697 (pmt) cc_final: 0.3765 (mmt) REVERT: E 626 MET cc_start: 0.2378 (OUTLIER) cc_final: 0.2105 (ttt) REVERT: K 23 GLU cc_start: 0.1478 (OUTLIER) cc_final: 0.1033 (tp30) REVERT: K 52 PRO cc_start: 0.4579 (Cg_endo) cc_final: 0.4377 (Cg_exo) REVERT: G 17 SER cc_start: 0.1157 (m) cc_final: 0.0609 (p) REVERT: G 29 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5488 (mt) REVERT: L 4 MET cc_start: 0.3821 (mtp) cc_final: 0.3499 (mmm) REVERT: L 42 LYS cc_start: 0.4069 (mmtm) cc_final: 0.3510 (pptt) REVERT: H 75 ILE cc_start: 0.4909 (OUTLIER) cc_final: 0.4594 (tp) REVERT: J 4 MET cc_start: 0.3217 (pmm) cc_final: 0.2343 (ptp) outliers start: 128 outliers final: 42 residues processed: 383 average time/residue: 1.0132 time to fit residues: 476.0152 Evaluate side-chains 322 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 435 TYR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 49 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 107 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 194 optimal weight: 0.0000 chunk 100 optimal weight: 5.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 117 GLN Q 80 HIS ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 99 ASN A 105 HIS ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN B 33 ASN B 280 ASN B 377 ASN C 66 HIS C 183 GLN C 315 GLN C 428 GLN D 607 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.161043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.141405 restraints weight = 69576.500| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 3.72 r_work: 0.4111 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4296 moved from start: 1.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 27874 Z= 0.252 Angle : 1.023 18.550 38227 Z= 0.483 Chirality : 0.056 0.450 4749 Planarity : 0.006 0.068 4481 Dihedral : 9.503 97.587 7562 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.81 % Allowed : 28.45 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.14), residues: 3031 helix: -1.02 (0.26), residues: 358 sheet: -0.33 (0.16), residues: 961 loop : -2.16 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 35 HIS 0.011 0.002 HIS N 90 PHE 0.025 0.003 PHE F 522 TYR 0.041 0.003 TYR C 384 ARG 0.016 0.001 ARG B 444 Details of bonding type rmsd link_NAG-ASN : bond 0.01370 ( 64) link_NAG-ASN : angle 3.82366 ( 192) link_ALPHA1-6 : bond 0.01010 ( 24) link_ALPHA1-6 : angle 1.95939 ( 72) link_BETA1-4 : bond 0.00704 ( 69) link_BETA1-4 : angle 2.30119 ( 207) link_ALPHA1-2 : bond 0.00803 ( 26) link_ALPHA1-2 : angle 1.86839 ( 78) link_ALPHA1-3 : bond 0.01177 ( 27) link_ALPHA1-3 : angle 2.22545 ( 81) hydrogen bonds : bond 0.04702 ( 772) hydrogen bonds : angle 6.46636 ( 2007) SS BOND : bond 0.00933 ( 47) SS BOND : angle 2.02531 ( 94) covalent geometry : bond 0.00547 (27617) covalent geometry : angle 0.96290 (37503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 338 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 47 TRP cc_start: 0.6727 (t60) cc_final: 0.6442 (t60) REVERT: O 65 LYS cc_start: 0.6887 (tptt) cc_final: 0.6643 (mmtt) REVERT: O 81 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5165 (tp) REVERT: P 42 GLN cc_start: 0.7443 (mt0) cc_final: 0.7238 (mt0) REVERT: P 104 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7046 (tppt) REVERT: M 18 LEU cc_start: -0.0107 (OUTLIER) cc_final: -0.0697 (pt) REVERT: M 51 MET cc_start: 0.2249 (mtm) cc_final: 0.1703 (mtp) REVERT: Q 28 ASP cc_start: 0.2802 (OUTLIER) cc_final: 0.2366 (t0) REVERT: Q 94 TYR cc_start: 0.2689 (m-10) cc_final: 0.1986 (m-10) REVERT: A 69 TRP cc_start: 0.4218 (OUTLIER) cc_final: 0.3095 (m100) REVERT: A 100 MET cc_start: 0.0633 (mtp) cc_final: -0.0457 (mmt) REVERT: A 104 MET cc_start: 0.2531 (mtt) cc_final: 0.1414 (tpt) REVERT: A 171 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5923 (mtpt) REVERT: A 247 CYS cc_start: 0.2909 (OUTLIER) cc_final: 0.2319 (p) REVERT: A 276 ASN cc_start: -0.1557 (OUTLIER) cc_final: -0.2680 (p0) REVERT: A 287 GLN cc_start: 0.2791 (mm-40) cc_final: 0.0833 (mm-40) REVERT: A 308 ARG cc_start: 0.3791 (OUTLIER) cc_final: 0.3469 (tmm160) REVERT: A 326 ILE cc_start: 0.4077 (OUTLIER) cc_final: 0.3872 (mm) REVERT: B 104 MET cc_start: 0.5762 (tmm) cc_final: 0.5494 (tmt) REVERT: B 162 THR cc_start: 0.8719 (p) cc_final: 0.8509 (p) REVERT: B 323 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7864 (pp) REVERT: B 475 MET cc_start: 0.7353 (mmp) cc_final: 0.6932 (mmt) REVERT: C 95 MET cc_start: 0.2514 (mtp) cc_final: 0.1945 (mtt) REVERT: C 96 TRP cc_start: 0.5586 (OUTLIER) cc_final: 0.5081 (m100) REVERT: C 100 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7336 (ptp) REVERT: C 166 ARG cc_start: 0.7106 (tmm160) cc_final: 0.5937 (ttt90) REVERT: D 537 LEU cc_start: 0.4107 (OUTLIER) cc_final: 0.2999 (tm) REVERT: D 591 GLN cc_start: 0.3227 (OUTLIER) cc_final: 0.2494 (mm110) REVERT: D 635 ILE cc_start: 0.3750 (OUTLIER) cc_final: 0.3501 (tp) REVERT: D 647 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.5197 (pt0) REVERT: K 23 GLU cc_start: 0.2116 (OUTLIER) cc_final: 0.1828 (tp30) REVERT: G 51 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7254 (tt) REVERT: G 63 PHE cc_start: 0.5653 (m-80) cc_final: 0.4457 (m-80) REVERT: G 66 ARG cc_start: 0.6018 (ptt180) cc_final: 0.5450 (ttp80) REVERT: G 101 ASP cc_start: 0.5057 (p0) cc_final: 0.4716 (t0) REVERT: I 82 LYS cc_start: 0.6661 (tmtt) cc_final: 0.6375 (tppp) REVERT: L 4 MET cc_start: 0.3931 (mtp) cc_final: 0.3571 (mmm) REVERT: L 35 TRP cc_start: 0.0993 (m-10) cc_final: 0.0436 (m100) REVERT: L 42 LYS cc_start: 0.4096 (mmtm) cc_final: 0.3459 (pptt) REVERT: H 46 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4837 (tp) REVERT: H 71 TYR cc_start: 0.4817 (m-80) cc_final: 0.4610 (m-80) REVERT: H 75 ILE cc_start: 0.5017 (OUTLIER) cc_final: 0.4710 (tp) REVERT: H 77 ASN cc_start: 0.7617 (t0) cc_final: 0.7379 (t0) REVERT: J 4 MET cc_start: 0.3564 (pmm) cc_final: 0.2633 (ptp) REVERT: J 89 GLN cc_start: 0.3784 (tp40) cc_final: 0.2140 (mt0) outliers start: 156 outliers final: 65 residues processed: 451 average time/residue: 1.0327 time to fit residues: 569.5214 Evaluate side-chains 368 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 282 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 96 TRP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 49 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 162 optimal weight: 0.0070 chunk 74 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 246 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 163 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 HIS R 101 GLN A 99 ASN A 105 HIS A 170 GLN A 216 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.161101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.141219 restraints weight = 68893.481| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.80 r_work: 0.4101 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4298 moved from start: 1.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27874 Z= 0.152 Angle : 0.897 13.507 38227 Z= 0.415 Chirality : 0.051 0.545 4749 Planarity : 0.005 0.102 4481 Dihedral : 8.877 94.916 7562 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.39 % Allowed : 30.69 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3031 helix: -0.57 (0.26), residues: 376 sheet: -0.13 (0.17), residues: 937 loop : -2.05 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 67 HIS 0.006 0.001 HIS P 90 PHE 0.033 0.002 PHE K 63 TYR 0.032 0.002 TYR I 76 ARG 0.014 0.001 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 64) link_NAG-ASN : angle 3.24164 ( 192) link_ALPHA1-6 : bond 0.00947 ( 24) link_ALPHA1-6 : angle 1.72143 ( 72) link_BETA1-4 : bond 0.00531 ( 69) link_BETA1-4 : angle 1.85327 ( 207) link_ALPHA1-2 : bond 0.00705 ( 26) link_ALPHA1-2 : angle 1.74156 ( 78) link_ALPHA1-3 : bond 0.01079 ( 27) link_ALPHA1-3 : angle 2.11032 ( 81) hydrogen bonds : bond 0.03797 ( 772) hydrogen bonds : angle 6.05803 ( 2007) SS BOND : bond 0.00526 ( 47) SS BOND : angle 1.90941 ( 94) covalent geometry : bond 0.00332 (27617) covalent geometry : angle 0.84606 (37503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 308 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 47 TRP cc_start: 0.6634 (t60) cc_final: 0.6294 (t60) REVERT: O 51 MET cc_start: 0.6793 (pmm) cc_final: 0.6401 (ptm) REVERT: O 65 LYS cc_start: 0.6899 (tptt) cc_final: 0.6677 (mmtt) REVERT: O 81 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5209 (tp) REVERT: P 36 TYR cc_start: 0.3245 (OUTLIER) cc_final: 0.2498 (t80) REVERT: P 42 GLN cc_start: 0.7465 (mt0) cc_final: 0.7233 (mt0) REVERT: P 88 CYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5046 (p) REVERT: M 20 LEU cc_start: 0.4295 (pp) cc_final: 0.3665 (mp) REVERT: M 51 MET cc_start: 0.2051 (mtm) cc_final: 0.1358 (tpp) REVERT: M 95 TYR cc_start: 0.1279 (m-80) cc_final: 0.0972 (m-80) REVERT: A 100 MET cc_start: 0.0576 (OUTLIER) cc_final: -0.0373 (mmt) REVERT: A 104 MET cc_start: 0.2421 (mtt) cc_final: 0.1009 (tpt) REVERT: A 247 CYS cc_start: 0.2795 (OUTLIER) cc_final: 0.1828 (p) REVERT: A 276 ASN cc_start: -0.1482 (OUTLIER) cc_final: -0.2587 (p0) REVERT: A 287 GLN cc_start: 0.2043 (mm-40) cc_final: 0.0268 (mm-40) REVERT: B 162 THR cc_start: 0.8786 (p) cc_final: 0.8578 (p) REVERT: B 323 ILE cc_start: 0.8369 (tp) cc_final: 0.7946 (pp) REVERT: B 475 MET cc_start: 0.7191 (mmp) cc_final: 0.6788 (mmt) REVERT: C 95 MET cc_start: 0.2967 (mtp) cc_final: 0.2562 (mtm) REVERT: C 100 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7075 (ptt) REVERT: C 164 GLU cc_start: 0.7422 (pm20) cc_final: 0.6318 (pm20) REVERT: C 166 ARG cc_start: 0.6744 (tmm160) cc_final: 0.5826 (ttt180) REVERT: C 258 GLN cc_start: 0.4675 (OUTLIER) cc_final: 0.4472 (mm-40) REVERT: D 535 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6139 (ttt) REVERT: D 537 LEU cc_start: 0.4101 (OUTLIER) cc_final: 0.3412 (tt) REVERT: D 591 GLN cc_start: 0.3390 (OUTLIER) cc_final: 0.2688 (mm110) REVERT: D 619 LEU cc_start: 0.3238 (OUTLIER) cc_final: 0.2951 (tm) REVERT: D 626 MET cc_start: 0.6065 (ptt) cc_final: 0.5146 (tmt) REVERT: E 542 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5244 (mpt180) REVERT: F 601 LYS cc_start: 0.4414 (mmmm) cc_final: 0.4199 (ttpt) REVERT: K 23 GLU cc_start: 0.2166 (OUTLIER) cc_final: 0.1777 (tp30) REVERT: G 51 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7301 (tt) REVERT: L 35 TRP cc_start: 0.0874 (m-10) cc_final: 0.0093 (m100) REVERT: L 36 TYR cc_start: 0.2337 (m-10) cc_final: 0.0534 (m-10) REVERT: H 75 ILE cc_start: 0.5244 (OUTLIER) cc_final: 0.4839 (tp) REVERT: H 77 ASN cc_start: 0.7419 (t0) cc_final: 0.7136 (t0) REVERT: J 4 MET cc_start: 0.3522 (pmm) cc_final: 0.2826 (ptp) REVERT: J 89 GLN cc_start: 0.3715 (tp40) cc_final: 0.2004 (mt0) outliers start: 118 outliers final: 55 residues processed: 386 average time/residue: 1.1900 time to fit residues: 566.0120 Evaluate side-chains 340 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 542 ARG Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 49 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 229 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 201 optimal weight: 0.2980 chunk 175 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 74 ASN Q 80 HIS ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 422 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.162796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.142453 restraints weight = 69457.609| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.88 r_work: 0.4110 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4816 moved from start: 1.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27874 Z= 0.189 Angle : 0.938 18.701 38227 Z= 0.442 Chirality : 0.053 0.620 4749 Planarity : 0.006 0.080 4481 Dihedral : 8.337 93.947 7562 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.39 % Allowed : 31.14 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3031 helix: -0.51 (0.26), residues: 363 sheet: -0.18 (0.17), residues: 954 loop : -2.09 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 631 HIS 0.101 0.003 HIS A 374 PHE 0.035 0.002 PHE K 63 TYR 0.026 0.002 TYR O 116 ARG 0.024 0.001 ARG G 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 64) link_NAG-ASN : angle 3.17217 ( 192) link_ALPHA1-6 : bond 0.00973 ( 24) link_ALPHA1-6 : angle 1.80214 ( 72) link_BETA1-4 : bond 0.00588 ( 69) link_BETA1-4 : angle 1.91675 ( 207) link_ALPHA1-2 : bond 0.00828 ( 26) link_ALPHA1-2 : angle 1.76552 ( 78) link_ALPHA1-3 : bond 0.01100 ( 27) link_ALPHA1-3 : angle 2.03314 ( 81) hydrogen bonds : bond 0.04114 ( 772) hydrogen bonds : angle 6.19250 ( 2007) SS BOND : bond 0.00699 ( 47) SS BOND : angle 1.93116 ( 94) covalent geometry : bond 0.00411 (27617) covalent geometry : angle 0.89067 (37503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 341 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 47 TRP cc_start: 0.6842 (OUTLIER) cc_final: 0.6339 (t60) REVERT: O 51 MET cc_start: 0.6936 (pmm) cc_final: 0.6684 (ptm) REVERT: O 65 LYS cc_start: 0.7081 (tptt) cc_final: 0.6855 (mmtt) REVERT: O 81 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5342 (tp) REVERT: P 17 GLU cc_start: 0.7594 (pp20) cc_final: 0.6175 (pm20) REVERT: P 18 ARG cc_start: 0.8423 (tpp80) cc_final: 0.7732 (tpp80) REVERT: P 36 TYR cc_start: 0.3446 (OUTLIER) cc_final: 0.2854 (t80) REVERT: P 42 GLN cc_start: 0.7434 (mt0) cc_final: 0.7215 (mt0) REVERT: P 104 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7380 (tppt) REVERT: M 45 LEU cc_start: 0.2843 (tp) cc_final: 0.2198 (mt) REVERT: M 51 MET cc_start: 0.2137 (mtm) cc_final: 0.1499 (mmm) REVERT: M 83 MET cc_start: 0.1011 (mpp) cc_final: -0.1308 (tpt) REVERT: Q 68 PHE cc_start: 0.4693 (OUTLIER) cc_final: 0.4426 (m-80) REVERT: R 4 MET cc_start: 0.1006 (tpp) cc_final: 0.0757 (tpp) REVERT: A 100 MET cc_start: 0.0773 (OUTLIER) cc_final: -0.0186 (mmt) REVERT: A 104 MET cc_start: 0.2738 (mtt) cc_final: 0.1376 (tpt) REVERT: A 247 CYS cc_start: 0.2894 (OUTLIER) cc_final: 0.2000 (p) REVERT: A 275 GLU cc_start: 0.0113 (OUTLIER) cc_final: -0.0146 (mp0) REVERT: A 276 ASN cc_start: -0.1745 (OUTLIER) cc_final: -0.2669 (p0) REVERT: A 287 GLN cc_start: 0.2587 (mm-40) cc_final: 0.1579 (mp10) REVERT: A 374 HIS cc_start: 0.2406 (OUTLIER) cc_final: 0.1632 (m-70) REVERT: A 475 MET cc_start: 0.2661 (mtm) cc_final: 0.2063 (mtt) REVERT: B 35 TRP cc_start: 0.5353 (m100) cc_final: 0.5090 (m100) REVERT: B 104 MET cc_start: 0.6451 (tmm) cc_final: 0.5893 (tmt) REVERT: B 161 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (mmm) REVERT: B 166 ARG cc_start: 0.6772 (mmt-90) cc_final: 0.6468 (tpt170) REVERT: B 255 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8615 (t) REVERT: B 323 ILE cc_start: 0.8643 (tp) cc_final: 0.8345 (pp) REVERT: C 100 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7525 (ptp) REVERT: C 104 MET cc_start: 0.3731 (mmt) cc_final: 0.3484 (tpp) REVERT: C 166 ARG cc_start: 0.6810 (tmm160) cc_final: 0.6012 (ttt180) REVERT: D 535 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6272 (ttt) REVERT: D 537 LEU cc_start: 0.3910 (OUTLIER) cc_final: 0.3261 (tm) REVERT: D 591 GLN cc_start: 0.3192 (OUTLIER) cc_final: 0.2578 (mm110) REVERT: D 626 MET cc_start: 0.6015 (ptt) cc_final: 0.5062 (tmt) REVERT: F 601 LYS cc_start: 0.5302 (mmmm) cc_final: 0.4874 (ttpt) REVERT: F 622 ILE cc_start: 0.5321 (OUTLIER) cc_final: 0.4978 (mp) REVERT: L 35 TRP cc_start: 0.1099 (m-10) cc_final: 0.0706 (m100) REVERT: L 36 TYR cc_start: 0.2835 (m-10) cc_final: 0.0780 (m-10) REVERT: H 75 ILE cc_start: 0.5329 (OUTLIER) cc_final: 0.4939 (tp) REVERT: J 4 MET cc_start: 0.3671 (pmm) cc_final: 0.3097 (ptp) outliers start: 118 outliers final: 54 residues processed: 419 average time/residue: 0.9874 time to fit residues: 509.4882 Evaluate side-chains 359 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 47 TRP Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 91 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 279 optimal weight: 0.0060 chunk 262 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 298 optimal weight: 0.0870 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.7376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 377 ASN C 98 ASN C 99 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.162772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.141885 restraints weight = 70086.547| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 3.89 r_work: 0.4106 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4983 moved from start: 1.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27874 Z= 0.160 Angle : 0.909 15.380 38227 Z= 0.421 Chirality : 0.050 0.539 4749 Planarity : 0.005 0.064 4481 Dihedral : 7.958 92.716 7562 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.54 % Allowed : 32.36 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 3031 helix: -0.65 (0.26), residues: 375 sheet: -0.10 (0.16), residues: 976 loop : -1.96 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 35 HIS 0.018 0.001 HIS A 374 PHE 0.032 0.002 PHE K 63 TYR 0.023 0.002 TYR H 71 ARG 0.015 0.001 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 64) link_NAG-ASN : angle 3.36962 ( 192) link_ALPHA1-6 : bond 0.00951 ( 24) link_ALPHA1-6 : angle 1.74858 ( 72) link_BETA1-4 : bond 0.00536 ( 69) link_BETA1-4 : angle 1.87387 ( 207) link_ALPHA1-2 : bond 0.00706 ( 26) link_ALPHA1-2 : angle 1.71427 ( 78) link_ALPHA1-3 : bond 0.01047 ( 27) link_ALPHA1-3 : angle 2.00128 ( 81) hydrogen bonds : bond 0.03775 ( 772) hydrogen bonds : angle 6.00785 ( 2007) SS BOND : bond 0.00438 ( 47) SS BOND : angle 2.01803 ( 94) covalent geometry : bond 0.00355 (27617) covalent geometry : angle 0.85690 (37503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 333 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 65 LYS cc_start: 0.7121 (tptt) cc_final: 0.6902 (mmtt) REVERT: O 81 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5374 (tp) REVERT: O 84 ASP cc_start: 0.7528 (m-30) cc_final: 0.6957 (p0) REVERT: O 99 ASP cc_start: 0.7112 (m-30) cc_final: 0.6868 (m-30) REVERT: P 17 GLU cc_start: 0.7550 (pp20) cc_final: 0.6185 (pm20) REVERT: P 18 ARG cc_start: 0.8486 (tpp80) cc_final: 0.7977 (tpp80) REVERT: P 36 TYR cc_start: 0.3427 (OUTLIER) cc_final: 0.2317 (t80) REVERT: P 42 GLN cc_start: 0.7539 (mt0) cc_final: 0.6870 (mp-120) REVERT: P 88 CYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5779 (p) REVERT: P 104 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7484 (tppt) REVERT: M 2 MET cc_start: 0.4820 (pmm) cc_final: 0.4411 (pmt) REVERT: M 20 LEU cc_start: 0.4685 (pp) cc_final: 0.4401 (mp) REVERT: M 51 MET cc_start: 0.2084 (mtm) cc_final: 0.1461 (tpp) REVERT: M 83 MET cc_start: 0.0722 (mpp) cc_final: -0.1292 (tpt) REVERT: Q 68 PHE cc_start: 0.4918 (OUTLIER) cc_final: 0.4537 (m-80) REVERT: R 4 MET cc_start: 0.1315 (tpp) cc_final: 0.1105 (tpp) REVERT: R 104 LYS cc_start: 0.5680 (tptp) cc_final: 0.5046 (mmmt) REVERT: A 100 MET cc_start: 0.0874 (OUTLIER) cc_final: 0.0026 (mmt) REVERT: A 104 MET cc_start: 0.2715 (mtt) cc_final: 0.1377 (tpt) REVERT: A 247 CYS cc_start: 0.3125 (OUTLIER) cc_final: 0.1878 (p) REVERT: A 276 ASN cc_start: -0.1099 (OUTLIER) cc_final: -0.2224 (p0) REVERT: A 287 GLN cc_start: 0.2321 (mm-40) cc_final: 0.2052 (mp10) REVERT: A 374 HIS cc_start: 0.1499 (OUTLIER) cc_final: 0.0552 (t-90) REVERT: B 66 HIS cc_start: 0.4536 (OUTLIER) cc_final: 0.4257 (p90) REVERT: B 104 MET cc_start: 0.6644 (tmm) cc_final: 0.6005 (tmt) REVERT: B 161 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8045 (mmm) REVERT: B 255 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8779 (t) REVERT: B 285 LEU cc_start: 0.8912 (mt) cc_final: 0.8689 (mp) REVERT: B 323 ILE cc_start: 0.8676 (tp) cc_final: 0.8441 (pp) REVERT: C 104 MET cc_start: 0.3948 (mmt) cc_final: 0.3729 (tpp) REVERT: C 141 ASP cc_start: 0.5739 (p0) cc_final: 0.5281 (p0) REVERT: C 166 ARG cc_start: 0.6598 (tmm160) cc_final: 0.5993 (ttt180) REVERT: D 537 LEU cc_start: 0.4045 (OUTLIER) cc_final: 0.3641 (tt) REVERT: D 591 GLN cc_start: 0.3331 (OUTLIER) cc_final: 0.2737 (mm110) REVERT: D 619 LEU cc_start: 0.3476 (OUTLIER) cc_final: 0.3206 (tm) REVERT: D 626 MET cc_start: 0.6050 (ptt) cc_final: 0.5025 (tmt) REVERT: F 530 MET cc_start: 0.4325 (ptp) cc_final: 0.4020 (pmm) REVERT: F 601 LYS cc_start: 0.5454 (mmmm) cc_final: 0.4808 (ttpp) REVERT: K 23 GLU cc_start: 0.2470 (OUTLIER) cc_final: 0.2040 (tp30) REVERT: K 82 LYS cc_start: 0.6482 (mmpt) cc_final: 0.6171 (mmtp) REVERT: H 53 LYS cc_start: 0.6996 (mtmm) cc_final: 0.6764 (mtmt) REVERT: H 75 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.4988 (tp) REVERT: J 4 MET cc_start: 0.3793 (pmm) cc_final: 0.3208 (ptp) outliers start: 95 outliers final: 50 residues processed: 400 average time/residue: 0.9456 time to fit residues: 470.8166 Evaluate side-chains 359 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain M residue 112 TRP Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 221 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 112 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 287 GLN C 422 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN G 46 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.163889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.142535 restraints weight = 69901.779| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.93 r_work: 0.4118 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5172 moved from start: 1.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27874 Z= 0.164 Angle : 0.954 21.823 38227 Z= 0.437 Chirality : 0.051 0.659 4749 Planarity : 0.005 0.060 4481 Dihedral : 7.784 90.784 7562 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.98 % Allowed : 33.78 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 3031 helix: -0.70 (0.26), residues: 375 sheet: 0.05 (0.17), residues: 959 loop : -1.97 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP J 67 HIS 0.036 0.001 HIS A 374 PHE 0.029 0.002 PHE K 63 TYR 0.030 0.002 TYR O 116 ARG 0.012 0.001 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 64) link_NAG-ASN : angle 4.03765 ( 192) link_ALPHA1-6 : bond 0.00947 ( 24) link_ALPHA1-6 : angle 1.73714 ( 72) link_BETA1-4 : bond 0.00535 ( 69) link_BETA1-4 : angle 1.81583 ( 207) link_ALPHA1-2 : bond 0.00670 ( 26) link_ALPHA1-2 : angle 1.71369 ( 78) link_ALPHA1-3 : bond 0.00997 ( 27) link_ALPHA1-3 : angle 1.94914 ( 81) hydrogen bonds : bond 0.03831 ( 772) hydrogen bonds : angle 6.03165 ( 2007) SS BOND : bond 0.00651 ( 47) SS BOND : angle 2.10792 ( 94) covalent geometry : bond 0.00367 (27617) covalent geometry : angle 0.89111 (37503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 324 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 65 LYS cc_start: 0.7101 (tptt) cc_final: 0.6879 (mmtt) REVERT: O 76 LYS cc_start: 0.7882 (tmmt) cc_final: 0.7634 (pptt) REVERT: O 81 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.5256 (tp) REVERT: O 84 ASP cc_start: 0.7738 (m-30) cc_final: 0.7016 (p0) REVERT: P 17 GLU cc_start: 0.7488 (pp20) cc_final: 0.6169 (pm20) REVERT: P 42 GLN cc_start: 0.7616 (mt0) cc_final: 0.6993 (mp-120) REVERT: P 79 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7609 (mm110) REVERT: P 104 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7752 (tppt) REVERT: M 20 LEU cc_start: 0.4860 (OUTLIER) cc_final: 0.4519 (mp) REVERT: M 45 LEU cc_start: 0.1619 (pt) cc_final: 0.0817 (mm) REVERT: M 51 MET cc_start: 0.2045 (mtm) cc_final: 0.1474 (tpp) REVERT: M 83 MET cc_start: 0.0802 (mpp) cc_final: -0.1180 (tpt) REVERT: M 93 VAL cc_start: 0.0671 (p) cc_final: 0.0245 (m) REVERT: M 95 TYR cc_start: 0.1251 (m-80) cc_final: 0.0920 (m-80) REVERT: R 4 MET cc_start: 0.1663 (tpp) cc_final: 0.1383 (tpp) REVERT: R 104 LYS cc_start: 0.5673 (tptp) cc_final: 0.5011 (mmmt) REVERT: A 100 MET cc_start: 0.0784 (OUTLIER) cc_final: 0.0055 (mmt) REVERT: A 104 MET cc_start: 0.2831 (mtt) cc_final: 0.1515 (tpt) REVERT: A 247 CYS cc_start: 0.3078 (OUTLIER) cc_final: 0.1756 (p) REVERT: A 276 ASN cc_start: -0.1226 (OUTLIER) cc_final: -0.2191 (p0) REVERT: A 434 MET cc_start: 0.4433 (ppp) cc_final: 0.2436 (tpt) REVERT: A 475 MET cc_start: 0.2791 (mtm) cc_final: 0.2192 (mtt) REVERT: B 66 HIS cc_start: 0.4623 (OUTLIER) cc_final: 0.4330 (p90) REVERT: B 104 MET cc_start: 0.6737 (tmm) cc_final: 0.6159 (tmt) REVERT: B 166 ARG cc_start: 0.4733 (tmt170) cc_final: 0.3288 (tmt-80) REVERT: B 255 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8906 (t) REVERT: B 273 ARG cc_start: 0.6739 (mmt90) cc_final: 0.6480 (mtp180) REVERT: B 285 LEU cc_start: 0.8935 (mt) cc_final: 0.8728 (mp) REVERT: C 166 ARG cc_start: 0.6643 (tmm160) cc_final: 0.6129 (ttt90) REVERT: D 537 LEU cc_start: 0.4043 (OUTLIER) cc_final: 0.3765 (tt) REVERT: D 619 LEU cc_start: 0.3407 (OUTLIER) cc_final: 0.3158 (tm) REVERT: D 626 MET cc_start: 0.6042 (ptt) cc_final: 0.4978 (tmt) REVERT: F 530 MET cc_start: 0.4737 (ptp) cc_final: 0.4247 (pmm) REVERT: K 23 GLU cc_start: 0.2769 (OUTLIER) cc_final: 0.2262 (tp30) REVERT: K 82 LYS cc_start: 0.6867 (mmpt) cc_final: 0.6547 (mmtp) REVERT: I 53 LYS cc_start: 0.7813 (ttmt) cc_final: 0.6872 (mppt) REVERT: L 36 TYR cc_start: 0.2892 (m-10) cc_final: 0.1018 (m-10) REVERT: L 103 ARG cc_start: 0.6676 (pmm150) cc_final: 0.6434 (mpp-170) REVERT: J 4 MET cc_start: 0.4032 (pmm) cc_final: 0.3693 (pmm) REVERT: J 39 ARG cc_start: 0.3348 (mmm160) cc_final: 0.3146 (mmm160) outliers start: 80 outliers final: 43 residues processed: 378 average time/residue: 0.9721 time to fit residues: 452.5345 Evaluate side-chains 345 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 112 TRP Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 298 optimal weight: 0.0370 chunk 44 optimal weight: 8.9990 chunk 297 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 224 optimal weight: 5.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN R 101 GLN A 105 HIS A 374 HIS C 287 GLN C 422 GLN C 462 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN G 46 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.164003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.142214 restraints weight = 70234.146| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 4.00 r_work: 0.4113 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 1.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27874 Z= 0.156 Angle : 0.941 21.592 38227 Z= 0.433 Chirality : 0.049 0.567 4749 Planarity : 0.005 0.062 4481 Dihedral : 7.522 88.227 7562 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.87 % Allowed : 34.67 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 3031 helix: -0.51 (0.26), residues: 375 sheet: 0.09 (0.17), residues: 956 loop : -1.91 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 35 HIS 0.008 0.001 HIS P 90 PHE 0.028 0.002 PHE K 63 TYR 0.037 0.002 TYR D 643 ARG 0.017 0.001 ARG P 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 64) link_NAG-ASN : angle 3.59544 ( 192) link_ALPHA1-6 : bond 0.00935 ( 24) link_ALPHA1-6 : angle 1.75153 ( 72) link_BETA1-4 : bond 0.00550 ( 69) link_BETA1-4 : angle 1.79861 ( 207) link_ALPHA1-2 : bond 0.00707 ( 26) link_ALPHA1-2 : angle 1.69575 ( 78) link_ALPHA1-3 : bond 0.00992 ( 27) link_ALPHA1-3 : angle 1.89560 ( 81) hydrogen bonds : bond 0.03652 ( 772) hydrogen bonds : angle 5.90639 ( 2007) SS BOND : bond 0.00435 ( 47) SS BOND : angle 2.52327 ( 94) covalent geometry : bond 0.00348 (27617) covalent geometry : angle 0.88491 (37503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23674.50 seconds wall clock time: 415 minutes 51.12 seconds (24951.12 seconds total)