Starting phenix.real_space_refine on Wed Jun 18 04:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fuu_3308/06_2025/5fuu_3308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fuu_3308/06_2025/5fuu_3308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5fuu_3308/06_2025/5fuu_3308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fuu_3308/06_2025/5fuu_3308.map" model { file = "/net/cci-nas-00/data/ceres_data/5fuu_3308/06_2025/5fuu_3308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fuu_3308/06_2025/5fuu_3308_neut.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 116 5.16 5 C 12882 2.51 5 N 3274 2.21 5 O 4463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20735 Number of models: 1 Model: "" Number of chains: 70 Chain: "A" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3553 Classifications: {'peptide': 449} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1150 Classifications: {'peptide': 144} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 141} Chain: "C" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3506 Classifications: {'peptide': 444} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1159 Classifications: {'peptide': 147} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3537 Classifications: {'peptide': 448} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1209 Classifications: {'peptide': 153} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 148} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} 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: "I" 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: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 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: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "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: 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: 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: "W" 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: "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: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} 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: "Z" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 160 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 3, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "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: 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: "g" 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: "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: 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: "j" 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: 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: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "y" 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: "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: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 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: "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: 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "7" 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: "8" 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: "9" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} 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: "AA" 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: "BA" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 149 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.89, per 1000 atoms: 0.62 Number of scatterers: 20735 At special positions: 0 Unit cell: (137.55, 153.27, 140.17, 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 116 16.00 O 4463 8.00 N 3274 7.00 C 12882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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 Atom "HETATM20028 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM18843 O5 NAG a 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN 8 4 " - " MAN 8 5 " " MAN O 4 " - " MAN O 5 " " MAN f 4 " - " MAN f 5 " " MAN p 4 " - " MAN p 5 " " MAN x 4 " - " MAN x 5 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA 8 3 " - " MAN 8 4 " " MAN 8 6 " - " MAN 8 7 " " BMA 9 3 " - " MAN 9 9 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA Y 3 " - " MAN Y 9 " " BMA Z 3 " - " MAN Z 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA p 3 " - " MAN p 4 " " MAN p 6 " - " MAN p 7 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " MAN y 6 " - " MAN y 7 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 6 3 " - " MAN 6 4 " " BMA 8 3 " - " MAN 8 6 " " MAN 8 6 " - " MAN 8 8 " " BMA 9 3 " - " MAN 9 4 " " BMA O 3 " - " MAN O 6 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 9 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 6 " " BMA p 3 " - " MAN p 6 " " MAN p 6 " - " MAN p 8 " " BMA x 3 " - " MAN x 6 " " BMA y 3 " - " MAN y 6 " " BMABA 3 " - " MANBA 9 " BETA1-2 " MAN 9 4 " - " NAG 9 5 " " MAN 9 9 " - " NAG 9 10 " " MAN Y 4 " - " NAG Y 5 " " MAN Y 9 " - " NAG Y 10 " " MAN Z 4 " - " NAG Z 5 " " MAN Z 9 " - " NAG Z 10 " " MANBA 4 " - " NAGBA 5 " " MANBA 9 " - " NAGBA 10 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG 9 5 " - " GAL 9 6 " " NAG 9 7 " - " GAL 9 8 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Y 5 " - " GAL Y 6 " " NAG Y 7 " - " GAL Y 8 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " MAN Z 4 " - " NAG Z 7 " " NAG Z 5 " - " GAL Z 6 " " NAG Z 7 " - " GAL Z 8 " " NAG Z 10 " - " GAL Z 11 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " 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 p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " MANBA 4 " - " NAGBA 7 " " NAGBA 5 " - " GALBA 6 " " NAGBA 7 " - " GALBA 8 " BETA1-6 " NAG 9 1 " - " FUC 9 11 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN 9 4 " - " NAG 9 7 " " NAG Y 1 " - " FUC Y 11 " " MAN Y 4 " - " NAG Y 7 " " NAG Z 1 " - " FUC Z 13 " " MAN Z 9 " - " NAG Z 12 " " NAG q 1 " - " FUC q 3 " " NAGBA 1 " - " FUCBA 12 " " MANBA 9 " - " NAGBA 11 " NAG-ASN " NAG 0 1 " - " ASN E 295 " " NAG 1 1 " - " ASN E 301 " " NAG 2 1 " - " ASN E 332 " " NAG 3 1 " - " ASN E 339 " " NAG 4 1 " - " ASN E 355 " " NAG 5 1 " - " ASN E 362 " " NAG 6 1 " - " ASN E 386 " " NAG 7 1 " - " ASN E 392 " " NAG 8 1 " - " ASN E 448 " " NAG 9 1 " - " ASN F 611 " " NAG A1135 " - " ASN A 135 " " NAG A1355 " - " ASN A 355 " " NAG A1397 " - " ASN A 397 " " NAG B1600 " - " ASN B 616 " " NAG B1625 " - " ASN B 625 " " NAG C1397 " - " ASN C 397 " " NAG D1600 " - " ASN D 616 " " NAG E1187 " - " ASN E 187 " " NAG E1397 " - " ASN E 397 " " NAG F1600 " - " ASN F 616 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 160 " " NAG K 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 301 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 339 " " NAG U 1 " - " ASN A 362 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN B 611 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN C 88 " " NAG b 1 " - " ASN C 135 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 241 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 276 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 339 " " NAG l 1 " - " ASN C 355 " " NAG m 1 " - " ASN C 362 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 392 " " NAG p 1 " - " ASN C 448 " " NAG q 1 " - " ASN D 611 " " NAG r 1 " - " ASN D 625 " " NAG s 1 " - " ASN D 637 " " NAG t 1 " - " ASN E 88 " " NAG u 1 " - " ASN E 135 " " NAG v 1 " - " ASN E 156 " " NAG w 1 " - " ASN E 160 " " NAG x 1 " - " ASN E 241 " " NAG y 1 " - " ASN E 262 " " NAG z 1 " - " ASN E 276 " " NAGAA 1 " - " ASN F 625 " " NAGBA 1 " - " ASN F 637 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 2.2 seconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 23.9% alpha, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.887A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 541 removed outlier: 6.551A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 4.110A pdb=" N ALA B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.802A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 634 removed outlier: 3.581A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 651 removed outlier: 4.402A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 663 removed outlier: 4.176A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.838A pdb=" N ILE C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.689A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.677A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.649A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 555 through 564 removed outlier: 3.511A pdb=" N GLN D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 597 removed outlier: 3.852A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 657 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.230A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 353 removed outlier: 3.590A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.720A pdb=" N PHE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.624A pdb=" N GLU E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 464 removed outlier: 3.711A pdb=" N ASN E 463 " --> pdb=" O ILE E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.272A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.738A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 566 removed outlier: 3.662A pdb=" N ARG F 557 " --> pdb=" O ASN F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.170A pdb=" N LEU F 592 " --> pdb=" O GLY F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.619A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'F' and resid 655 through 662 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.726A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing sheet with id=AA, first strand: chain 'A' and resid 494 through 497 removed outlier: 4.216A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AD, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AE, first strand: chain 'A' and resid 171 through 177 removed outlier: 4.593A pdb=" N SER A 190 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AG, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.052A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 381 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 383 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.992A pdb=" N PHE A 382 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 419 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.052A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 381 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 383 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.992A pdb=" N PHE A 382 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 419 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU A 260 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.052A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 381 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 383 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.992A pdb=" N PHE A 382 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 419 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 260 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.792A pdb=" N ASN A 302 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE A 322 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A 304 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY A 321 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER A 306 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A 319 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N HIS A 308 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 317 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.141A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.080A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=CD, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=CE, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.741A pdb=" N ARG C 192 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=CG, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=CH, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.982A pdb=" N LEU C 260 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing sheet with id=CI, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=CJ, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.335A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.975A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=CK, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.335A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=CL, first strand: chain 'C' and resid 301 through 308 removed outlier: 7.193A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 513 through 515 Processing sheet with id=EA, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.181A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.934A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=ED, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=EE, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.972A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=EF, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=EG, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=EH, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.927A pdb=" N LEU E 260 " --> pdb=" O ASN E 448 " (cutoff:3.500A) Processing sheet with id=EI, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=EJ, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.074A pdb=" N PHE E 383 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS E 385 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS E 331 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE E 333 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 13.518A pdb=" N CYS E 418 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 13.624A pdb=" N HIS E 330 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN E 295 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR E 297 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.018A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=EK, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.074A pdb=" N PHE E 383 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS E 385 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS E 331 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE E 333 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 13.518A pdb=" N CYS E 418 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 13.624A pdb=" N HIS E 330 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN E 295 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR E 297 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing sheet with id=EL, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.755A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=FA, first strand: chain 'F' and resid 513 through 515 Processing sheet with id=HA, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=HB, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.158A pdb=" N THR H 108 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=HC, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.158A pdb=" N THR H 108 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=HD, first strand: chain 'H' and resid 100R through 103 removed outlier: 6.940A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing sheet with id=LA, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.599A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=LB, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.694A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=LC, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.872A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing sheet with id=LD, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.694A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=MA, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=MB, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.076A pdb=" N THR M 108 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=MC, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.076A pdb=" N THR M 108 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=MD, first strand: chain 'M' and resid 100R through 103 removed outlier: 6.661A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) Processing sheet with id=NA, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=NB, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=NC, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.142A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=ND, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=NE, first strand: chain 'N' and resid 27C through 27D removed outlier: 3.678A pdb=" N LYS N 30 " --> pdb=" O GLN N 27D" (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2016 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: 7.53 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4977 1.33 - 1.45: 5227 1.45 - 1.57: 10733 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 21101 Sorted by residual: bond pdb=" CA ASN A 229 " pdb=" CB ASN A 229 " ideal model delta sigma weight residual 1.530 1.412 0.117 1.64e-02 3.72e+03 5.11e+01 bond pdb=" N PRO E 118 " pdb=" CD PRO E 118 " ideal model delta sigma weight residual 1.473 1.553 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" N PRO A 118 " pdb=" CD PRO A 118 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.91e+01 bond pdb=" CA SER F 599 " pdb=" C SER F 599 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.28e-02 6.10e+03 2.58e+01 bond pdb=" C ASN E 80 " pdb=" N PRO E 81 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.11e-02 8.12e+03 2.45e+01 ... (remaining 21096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 25249 2.61 - 5.21: 2560 5.21 - 7.82: 625 7.82 - 10.43: 169 10.43 - 13.03: 27 Bond angle restraints: 28630 Sorted by residual: angle pdb=" C GLY M 100 " pdb=" N PRO M 100A" pdb=" CA PRO M 100A" ideal model delta sigma weight residual 119.66 128.29 -8.63 7.30e-01 1.88e+00 1.40e+02 angle pdb=" C ASN C 80 " pdb=" N PRO C 81 " pdb=" CA PRO C 81 " ideal model delta sigma weight residual 119.99 130.47 -10.48 1.08e+00 8.57e-01 9.42e+01 angle pdb=" C GLY C 237 " pdb=" N PRO C 238 " pdb=" CA PRO C 238 " ideal model delta sigma weight residual 119.76 128.86 -9.10 1.00e+00 1.00e+00 8.29e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.32 129.28 -9.96 1.14e+00 7.69e-01 7.64e+01 angle pdb=" C ALA C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.66 125.92 -6.26 7.20e-01 1.93e+00 7.57e+01 ... (remaining 28625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 14752 26.70 - 53.39: 271 53.39 - 80.09: 230 80.09 - 106.78: 135 106.78 - 133.48: 4 Dihedral angle restraints: 15392 sinusoidal: 8822 harmonic: 6570 Sorted by residual: dihedral pdb=" CA ASN E 412 " pdb=" C ASN E 412 " pdb=" N THR E 413 " pdb=" CA THR E 413 " ideal model delta harmonic sigma weight residual -180.00 -46.52 -133.48 0 5.00e+00 4.00e-02 7.13e+02 dihedral pdb=" CA VAL C 65 " pdb=" C VAL C 65 " pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta harmonic sigma weight residual 0.00 -37.56 37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" C GLN C 352 " pdb=" N GLN C 352 " pdb=" CA GLN C 352 " pdb=" CB GLN C 352 " ideal model delta harmonic sigma weight residual -122.60 -140.88 18.28 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 15389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 3170 0.158 - 0.317: 638 0.317 - 0.475: 19 0.475 - 0.634: 13 0.634 - 0.792: 10 Chirality restraints: 3850 Sorted by residual: chirality pdb=" C1 MAN f 7 " pdb=" O3 MAN f 6 " pdb=" C2 MAN f 7 " pdb=" O5 MAN f 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 MAN O 7 " pdb=" O3 MAN O 6 " pdb=" C2 MAN O 7 " pdb=" O5 MAN O 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 chirality pdb=" C1 MAN y 7 " pdb=" O3 MAN y 6 " pdb=" C2 MAN y 7 " pdb=" O5 MAN y 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 ... (remaining 3847 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 301 " -0.300 2.00e-02 2.50e+03 3.39e-01 1.44e+03 pdb=" CG ASN C 301 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 301 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 301 " 0.505 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.446 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 156 " 0.258 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN A 156 " -0.143 2.00e-02 2.50e+03 pdb=" OD1 ASN A 156 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 156 " -0.526 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.450 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.308 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" CG ASN C 156 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " 0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.474 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " -0.440 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 173 2.48 - 3.08: 15649 3.08 - 3.69: 28449 3.69 - 4.29: 44804 4.29 - 4.90: 70198 Nonbonded interactions: 159273 Sorted by model distance: nonbonded pdb=" CA PRO E 183 " pdb=" CD1 TYR E 191 " model vdw 1.869 3.770 nonbonded pdb=" OD1 ASN A 339 " pdb=" N ASP A 340 " model vdw 1.900 3.120 nonbonded pdb=" O ALA E 336 " pdb=" OD1 ASN E 339 " model vdw 1.967 3.040 nonbonded pdb=" OE1 GLU A 87 " pdb=" O7 NAG G 1 " model vdw 1.996 3.040 nonbonded pdb=" O3 GAL Y 6 " pdb=" O2 MAN x 6 " model vdw 2.000 3.040 ... (remaining 159268 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 '1' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain 'AA' selection = chain 'G' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'z' } ncs_group { reference = (chain '2' and resid 1 through 2) selection = (chain '7' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) } ncs_group { reference = (chain '8' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'f' and (resid 1 or resid 4 through 7)) selection = (chain 'p' and (resid 2 or resid 5 through 8)) selection = (chain 'y' and (resid 1 or resid 4 through 7)) } ncs_group { reference = (chain '9' and (resid 1 or resid 10 through 11)) selection = (chain 'BA' and (resid 2 or resid 11 through 12)) selection = (chain 'Y' and (resid 1 or resid 10 through 11)) } ncs_group { reference = (chain 'A' and (resid 31 through 136 or resid 152 through 401 or resid 410 throu \ gh 506 or resid 1397)) selection = (chain 'C' and (resid 31 through 57 or resid 64 through 401 or resid 410 through \ 506 or resid 1397)) selection = (chain 'E' and (resid 31 through 57 or resid 64 through 136 or resid 152 through \ 401 or resid 410 through 506 or resid 1397)) } ncs_group { reference = (chain 'B' and resid 521 through 658) selection = (chain 'D' and resid 521 through 658) selection = (chain 'F' and resid 521 through 658) } ncs_group { reference = (chain 'H' and resid 2 through 113) selection = (chain 'M' and resid 2 through 113) } ncs_group { reference = (chain 'L' and resid 2 through 108) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 49.290 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.015 0.432 21349 Z= 0.942 Angle : 2.291 44.759 29337 Z= 1.150 Chirality : 0.120 0.792 3850 Planarity : 0.017 0.137 3338 Dihedral : 17.626 133.475 11050 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 1.69 % Allowed : 6.15 % Favored : 92.15 % Rotamer: Outliers : 1.20 % Allowed : 1.54 % Favored : 97.26 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.38 (0.15), residues: 2243 helix: -1.70 (0.20), residues: 431 sheet: -1.02 (0.20), residues: 600 loop : -1.82 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 100G HIS 0.003 0.000 HIS C 330 PHE 0.010 0.000 PHE B 522 TYR 0.003 0.000 TYR M 100N ARG 0.007 0.003 ARG C 503 Details of bonding type rmsd link_NAG-ASN : bond 0.03983 ( 64) link_NAG-ASN : angle 13.55689 ( 192) link_ALPHA1-6 : bond 0.04268 ( 14) link_ALPHA1-6 : angle 5.20510 ( 42) link_BETA1-2 : bond 0.03276 ( 8) link_BETA1-2 : angle 3.54094 ( 24) link_BETA1-4 : bond 0.04159 ( 96) link_BETA1-4 : angle 5.50298 ( 288) link_ALPHA1-2 : bond 0.02252 ( 6) link_ALPHA1-2 : angle 3.06926 ( 18) link_ALPHA1-3 : bond 0.03391 ( 16) link_ALPHA1-3 : angle 5.13624 ( 48) hydrogen bonds : bond 0.17019 ( 688) hydrogen bonds : angle 8.33279 ( 2016) link_BETA1-6 : bond 0.03395 ( 9) link_BETA1-6 : angle 3.45882 ( 27) SS BOND : bond 0.00679 ( 34) SS BOND : angle 10.55215 ( 68) covalent geometry : bond 0.01402 (21101) covalent geometry : angle 1.86196 (28630) Misc. bond : bond 0.43203 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 562 time to evaluate : 2.380 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: A 96 TRP cc_start: 0.8288 (m-90) cc_final: 0.7339 (m-10) REVERT: A 100 MET cc_start: 0.8292 (mtp) cc_final: 0.8077 (mtm) REVERT: A 115 SER cc_start: 0.8924 (p) cc_final: 0.8719 (p) REVERT: A 229 ASN cc_start: 0.6352 (m110) cc_final: 0.5970 (m110) REVERT: A 434 MET cc_start: 0.8581 (tmm) cc_final: 0.8283 (ttm) REVERT: A 499 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6459 (t) REVERT: B 543 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 554 ASN cc_start: 0.7501 (m-40) cc_final: 0.7024 (t0) REVERT: B 606 THR cc_start: 0.8556 (t) cc_final: 0.8325 (p) REVERT: B 628 TRP cc_start: 0.8507 (t-100) cc_final: 0.8269 (t-100) REVERT: B 663 LEU cc_start: 0.7516 (mt) cc_final: 0.7282 (mt) REVERT: C 100 MET cc_start: 0.7585 (mtp) cc_final: 0.7276 (mtm) REVERT: C 297 THR cc_start: 0.7138 (p) cc_final: 0.6856 (p) REVERT: C 434 MET cc_start: 0.8329 (ppp) cc_final: 0.8116 (ptp) REVERT: C 482 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7441 (mm-30) REVERT: D 584 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7313 (mt-10) REVERT: E 42 VAL cc_start: 0.9667 (t) cc_final: 0.9447 (p) REVERT: E 45 TRP cc_start: 0.7838 (m-10) cc_final: 0.7631 (m-10) REVERT: E 56 SER cc_start: 0.9043 (p) cc_final: 0.8819 (m) REVERT: E 57 ASP cc_start: 0.7473 (t0) cc_final: 0.7104 (t70) REVERT: E 213 ILE cc_start: 0.9177 (mt) cc_final: 0.8879 (tt) REVERT: F 629 MET cc_start: 0.7662 (mtm) cc_final: 0.6197 (mtm) REVERT: H 22 CYS cc_start: 0.3418 (t) cc_final: 0.2751 (t) REVERT: M 82 MET cc_start: 0.6699 (mtm) cc_final: 0.6449 (mtp) outliers start: 24 outliers final: 11 residues processed: 583 average time/residue: 0.3769 time to fit residues: 317.8634 Evaluate side-chains 247 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS C 389 GLN D 624 ASN E 66 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065603 restraints weight = 65430.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067437 restraints weight = 39729.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068688 restraints weight = 28843.303| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21349 Z= 0.192 Angle : 1.115 18.695 29337 Z= 0.488 Chirality : 0.058 0.821 3850 Planarity : 0.005 0.045 3338 Dihedral : 15.459 84.200 6745 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.76 % Allowed : 4.41 % Favored : 94.83 % Rotamer: Outliers : 0.25 % Allowed : 2.24 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.47 (0.16), residues: 2243 helix: -0.37 (0.24), residues: 434 sheet: -0.64 (0.21), residues: 577 loop : -1.35 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 479 HIS 0.006 0.001 HIS A 374 PHE 0.020 0.002 PHE C 53 TYR 0.019 0.002 TYR E 191 ARG 0.013 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00890 ( 64) link_NAG-ASN : angle 5.36971 ( 192) link_ALPHA1-6 : bond 0.00772 ( 14) link_ALPHA1-6 : angle 1.96551 ( 42) link_BETA1-2 : bond 0.00655 ( 8) link_BETA1-2 : angle 1.88502 ( 24) link_BETA1-4 : bond 0.00703 ( 96) link_BETA1-4 : angle 2.87886 ( 288) link_ALPHA1-2 : bond 0.00729 ( 6) link_ALPHA1-2 : angle 1.48427 ( 18) link_ALPHA1-3 : bond 0.01466 ( 16) link_ALPHA1-3 : angle 1.96961 ( 48) hydrogen bonds : bond 0.05681 ( 688) hydrogen bonds : angle 6.39140 ( 2016) link_BETA1-6 : bond 0.00536 ( 9) link_BETA1-6 : angle 1.81978 ( 27) SS BOND : bond 0.00452 ( 34) SS BOND : angle 1.59074 ( 68) covalent geometry : bond 0.00389 (21101) covalent geometry : angle 0.98580 (28630) Misc. bond : bond 0.00412 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 373 time to evaluate : 2.090 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: A 94 ASN cc_start: 0.8591 (t0) cc_final: 0.8180 (t0) REVERT: A 96 TRP cc_start: 0.8344 (m-90) cc_final: 0.7504 (m-10) REVERT: A 373 MET cc_start: 0.7761 (mmp) cc_final: 0.7364 (mmp) REVERT: A 426 MET cc_start: 0.8769 (tpt) cc_final: 0.7970 (tpp) REVERT: A 499 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7510 (t) REVERT: B 628 TRP cc_start: 0.8604 (t-100) cc_final: 0.8293 (t-100) REVERT: B 655 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8956 (mmmm) REVERT: C 34 LEU cc_start: 0.8980 (mt) cc_final: 0.8764 (mp) REVERT: C 297 THR cc_start: 0.8135 (p) cc_final: 0.7877 (p) REVERT: C 482 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8304 (mm-30) REVERT: D 530 MET cc_start: 0.7748 (mtm) cc_final: 0.7172 (mpp) REVERT: D 536 THR cc_start: 0.8573 (p) cc_final: 0.8169 (p) REVERT: D 540 GLN cc_start: 0.8484 (mp10) cc_final: 0.8203 (mp10) REVERT: D 626 MET cc_start: 0.8759 (tpp) cc_final: 0.7897 (tpp) REVERT: D 629 MET cc_start: 0.7289 (tpp) cc_final: 0.6996 (tpp) REVERT: D 651 ASN cc_start: 0.8798 (m110) cc_final: 0.8574 (m-40) REVERT: E 42 VAL cc_start: 0.9500 (t) cc_final: 0.9256 (p) REVERT: E 45 TRP cc_start: 0.8198 (m-10) cc_final: 0.7893 (m-10) REVERT: E 318 TYR cc_start: 0.8120 (m-80) cc_final: 0.7841 (m-80) REVERT: E 484 TYR cc_start: 0.8983 (p90) cc_final: 0.8699 (p90) REVERT: E 486 TYR cc_start: 0.9121 (m-80) cc_final: 0.8801 (m-10) REVERT: F 520 LEU cc_start: 0.8466 (tp) cc_final: 0.8129 (tp) REVERT: F 629 MET cc_start: 0.8247 (mtm) cc_final: 0.6518 (mtm) REVERT: F 655 LYS cc_start: 0.8762 (tppt) cc_final: 0.8479 (mmtp) REVERT: F 658 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8457 (tm-30) REVERT: H 31 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8589 (mtpt) REVERT: H 45 LEU cc_start: 0.9252 (mt) cc_final: 0.8881 (mt) REVERT: H 100 ASP cc_start: 0.9272 (t0) cc_final: 0.8900 (t0) REVERT: L 34 TYR cc_start: 0.9029 (m-80) cc_final: 0.8817 (m-80) REVERT: L 36 TYR cc_start: 0.7838 (m-80) cc_final: 0.7036 (m-80) REVERT: M 95 MET cc_start: 0.8524 (ttm) cc_final: 0.8203 (ttm) REVERT: N 27 GLU cc_start: 0.8395 (tp30) cc_final: 0.7877 (tp30) outliers start: 5 outliers final: 0 residues processed: 374 average time/residue: 0.3228 time to fit residues: 188.2831 Evaluate side-chains 228 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 96 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 164 optimal weight: 0.0050 chunk 138 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 246 GLN B 553 ASN E 249 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 76 ASN M 97 GLN ** N 6 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 = 0.3397 r_free = 0.3397 target = 0.081429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063076 restraints weight = 67043.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.064820 restraints weight = 41444.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066003 restraints weight = 30497.881| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21349 Z= 0.197 Angle : 1.019 29.059 29337 Z= 0.443 Chirality : 0.054 0.534 3850 Planarity : 0.004 0.041 3338 Dihedral : 12.822 78.280 6745 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.26 % Favored : 94.07 % Rotamer: Outliers : 0.25 % Allowed : 1.59 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.29 (0.17), residues: 2243 helix: -0.29 (0.24), residues: 441 sheet: -0.55 (0.20), residues: 614 loop : -1.20 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 103 HIS 0.006 0.001 HIS C 330 PHE 0.016 0.002 PHE E 53 TYR 0.015 0.001 TYR D 638 ARG 0.005 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 64) link_NAG-ASN : angle 4.37822 ( 192) link_ALPHA1-6 : bond 0.00781 ( 14) link_ALPHA1-6 : angle 2.06855 ( 42) link_BETA1-2 : bond 0.00570 ( 8) link_BETA1-2 : angle 1.75992 ( 24) link_BETA1-4 : bond 0.00437 ( 96) link_BETA1-4 : angle 2.60751 ( 288) link_ALPHA1-2 : bond 0.00701 ( 6) link_ALPHA1-2 : angle 1.60431 ( 18) link_ALPHA1-3 : bond 0.01262 ( 16) link_ALPHA1-3 : angle 1.62817 ( 48) hydrogen bonds : bond 0.05099 ( 688) hydrogen bonds : angle 5.99611 ( 2016) link_BETA1-6 : bond 0.00505 ( 9) link_BETA1-6 : angle 1.69032 ( 27) SS BOND : bond 0.00472 ( 34) SS BOND : angle 1.64894 ( 68) covalent geometry : bond 0.00421 (21101) covalent geometry : angle 0.91766 (28630) Misc. bond : bond 0.00216 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 321 time to evaluate : 2.053 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: A 94 ASN cc_start: 0.8620 (t0) cc_final: 0.8366 (t0) REVERT: A 96 TRP cc_start: 0.8451 (m-90) cc_final: 0.7635 (m-10) REVERT: B 629 MET cc_start: 0.8443 (tpp) cc_final: 0.7806 (tpp) REVERT: B 655 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8946 (mmmm) REVERT: C 100 MET cc_start: 0.8679 (mtm) cc_final: 0.8435 (mtm) REVERT: C 297 THR cc_start: 0.8051 (p) cc_final: 0.7798 (p) REVERT: C 373 MET cc_start: 0.8740 (mmm) cc_final: 0.8391 (mmt) REVERT: C 482 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8443 (mm-30) REVERT: D 530 MET cc_start: 0.7823 (mtm) cc_final: 0.7080 (mpp) REVERT: D 603 ILE cc_start: 0.9491 (mt) cc_final: 0.9205 (mt) REVERT: D 626 MET cc_start: 0.8961 (tpp) cc_final: 0.7578 (tpt) REVERT: D 636 ASP cc_start: 0.8903 (t70) cc_final: 0.8696 (t0) REVERT: D 641 GLU cc_start: 0.8495 (mp0) cc_final: 0.8272 (mp0) REVERT: D 647 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7697 (mp0) REVERT: E 42 VAL cc_start: 0.9583 (t) cc_final: 0.9365 (p) REVERT: E 318 TYR cc_start: 0.8025 (m-80) cc_final: 0.7702 (m-80) REVERT: E 484 TYR cc_start: 0.8978 (p90) cc_final: 0.8631 (p90) REVERT: E 486 TYR cc_start: 0.9138 (m-80) cc_final: 0.8742 (m-80) REVERT: E 505 VAL cc_start: 0.8466 (p) cc_final: 0.8155 (p) REVERT: F 658 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8557 (tm-30) REVERT: H 31 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8091 (mtpt) REVERT: H 72 ASP cc_start: 0.7945 (t0) cc_final: 0.7712 (t0) REVERT: H 98 GLU cc_start: 0.7603 (tt0) cc_final: 0.7326 (tt0) REVERT: H 100 ASP cc_start: 0.9452 (t0) cc_final: 0.9157 (t0) REVERT: L 27 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7641 (tpp80) REVERT: L 77 ARG cc_start: 0.8113 (mpp80) cc_final: 0.7887 (mpp80) REVERT: M 82 MET cc_start: 0.8455 (mtp) cc_final: 0.8245 (mtm) REVERT: M 97 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6278 (tm-30) REVERT: M 100 MET cc_start: 0.8951 (mpp) cc_final: 0.8685 (mpp) REVERT: N 27 GLU cc_start: 0.8394 (tp30) cc_final: 0.7963 (tp30) outliers start: 5 outliers final: 2 residues processed: 325 average time/residue: 0.3003 time to fit residues: 152.1603 Evaluate side-chains 222 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 78 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061820 restraints weight = 67869.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063507 restraints weight = 42176.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064668 restraints weight = 31141.008| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21349 Z= 0.195 Angle : 0.942 31.228 29337 Z= 0.415 Chirality : 0.052 0.455 3850 Planarity : 0.004 0.049 3338 Dihedral : 10.705 70.907 6745 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.84 % Favored : 93.71 % Rotamer: Outliers : 0.15 % Allowed : 2.59 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.14 (0.17), residues: 2243 helix: 0.01 (0.25), residues: 440 sheet: -0.45 (0.20), residues: 605 loop : -1.19 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 631 HIS 0.007 0.001 HIS C 330 PHE 0.015 0.002 PHE B 522 TYR 0.016 0.002 TYR D 638 ARG 0.005 0.001 ARG B 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 64) link_NAG-ASN : angle 3.63049 ( 192) link_ALPHA1-6 : bond 0.00811 ( 14) link_ALPHA1-6 : angle 1.96427 ( 42) link_BETA1-2 : bond 0.00461 ( 8) link_BETA1-2 : angle 1.76926 ( 24) link_BETA1-4 : bond 0.00423 ( 96) link_BETA1-4 : angle 2.42938 ( 288) link_ALPHA1-2 : bond 0.00712 ( 6) link_ALPHA1-2 : angle 1.59811 ( 18) link_ALPHA1-3 : bond 0.01162 ( 16) link_ALPHA1-3 : angle 1.68646 ( 48) hydrogen bonds : bond 0.04644 ( 688) hydrogen bonds : angle 5.78238 ( 2016) link_BETA1-6 : bond 0.00421 ( 9) link_BETA1-6 : angle 1.66998 ( 27) SS BOND : bond 0.00580 ( 34) SS BOND : angle 1.62987 ( 68) covalent geometry : bond 0.00417 (21101) covalent geometry : angle 0.85900 (28630) Misc. bond : bond 0.00268 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 2.103 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: A 96 TRP cc_start: 0.8584 (m-90) cc_final: 0.7663 (m-90) REVERT: A 104 MET cc_start: 0.8836 (tpp) cc_final: 0.8615 (tpp) REVERT: A 217 TYR cc_start: 0.8006 (m-80) cc_final: 0.7254 (m-80) REVERT: B 629 MET cc_start: 0.8117 (tpp) cc_final: 0.7566 (tpp) REVERT: C 100 MET cc_start: 0.8662 (mtm) cc_final: 0.8343 (mtm) REVERT: C 373 MET cc_start: 0.8717 (mmm) cc_final: 0.8441 (mmp) REVERT: C 482 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8490 (mm-30) REVERT: D 530 MET cc_start: 0.8003 (mtm) cc_final: 0.7301 (mpp) REVERT: D 536 THR cc_start: 0.8527 (p) cc_final: 0.7471 (p) REVERT: D 559 ILE cc_start: 0.9045 (mt) cc_final: 0.8757 (mt) REVERT: D 626 MET cc_start: 0.8979 (tpp) cc_final: 0.7934 (tmm) REVERT: D 641 GLU cc_start: 0.8502 (mp0) cc_final: 0.8246 (mp0) REVERT: D 647 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7682 (mp0) REVERT: E 318 TYR cc_start: 0.8116 (m-80) cc_final: 0.7810 (m-80) REVERT: E 484 TYR cc_start: 0.8916 (p90) cc_final: 0.8518 (p90) REVERT: E 505 VAL cc_start: 0.8389 (p) cc_final: 0.7852 (p) REVERT: F 530 MET cc_start: 0.8995 (ttp) cc_final: 0.8529 (ttp) REVERT: F 642 ILE cc_start: 0.9598 (mt) cc_final: 0.9352 (mm) REVERT: H 31 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8039 (mtpt) REVERT: H 67 PHE cc_start: 0.8082 (m-80) cc_final: 0.7699 (m-80) REVERT: H 72 ASP cc_start: 0.7851 (t0) cc_final: 0.7359 (t70) REVERT: H 82 MET cc_start: 0.8013 (mtt) cc_final: 0.7808 (mtt) REVERT: H 98 GLU cc_start: 0.7517 (tt0) cc_final: 0.7218 (tt0) REVERT: H 100 ASP cc_start: 0.9532 (t0) cc_final: 0.9312 (t0) REVERT: L 36 TYR cc_start: 0.8063 (m-80) cc_final: 0.6848 (m-80) REVERT: L 82 ASP cc_start: 0.7551 (m-30) cc_final: 0.7340 (m-30) REVERT: M 35 TYR cc_start: 0.8499 (m-10) cc_final: 0.8184 (m-10) REVERT: M 95 MET cc_start: 0.8675 (ttm) cc_final: 0.7589 (ttp) REVERT: M 100 MET cc_start: 0.9057 (mpp) cc_final: 0.8741 (mpp) REVERT: N 4 MET cc_start: 0.6888 (mmp) cc_final: 0.6636 (tpp) REVERT: N 27 GLU cc_start: 0.8443 (tp30) cc_final: 0.8031 (tp30) outliers start: 3 outliers final: 1 residues processed: 307 average time/residue: 0.3058 time to fit residues: 146.9042 Evaluate side-chains 226 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 215 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 0.0770 chunk 79 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN H 39 GLN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.059780 restraints weight = 69101.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062120 restraints weight = 42919.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.062714 restraints weight = 28037.980| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21349 Z= 0.245 Angle : 0.974 27.900 29337 Z= 0.435 Chirality : 0.053 0.479 3850 Planarity : 0.005 0.050 3338 Dihedral : 10.079 65.781 6745 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.69 % Favored : 92.91 % Rotamer: Outliers : 0.10 % Allowed : 2.14 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.36 (0.17), residues: 2243 helix: -0.17 (0.25), residues: 439 sheet: -0.62 (0.20), residues: 625 loop : -1.31 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 45 HIS 0.008 0.002 HIS A 374 PHE 0.021 0.002 PHE H 27 TYR 0.019 0.002 TYR D 638 ARG 0.006 0.001 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 64) link_NAG-ASN : angle 3.62540 ( 192) link_ALPHA1-6 : bond 0.00824 ( 14) link_ALPHA1-6 : angle 1.94217 ( 42) link_BETA1-2 : bond 0.00521 ( 8) link_BETA1-2 : angle 2.16609 ( 24) link_BETA1-4 : bond 0.00392 ( 96) link_BETA1-4 : angle 2.24844 ( 288) link_ALPHA1-2 : bond 0.00714 ( 6) link_ALPHA1-2 : angle 1.60537 ( 18) link_ALPHA1-3 : bond 0.01136 ( 16) link_ALPHA1-3 : angle 1.73786 ( 48) hydrogen bonds : bond 0.04767 ( 688) hydrogen bonds : angle 5.78997 ( 2016) link_BETA1-6 : bond 0.00761 ( 9) link_BETA1-6 : angle 2.07860 ( 27) SS BOND : bond 0.00455 ( 34) SS BOND : angle 1.64765 ( 68) covalent geometry : bond 0.00541 (21101) covalent geometry : angle 0.89755 (28630) Misc. bond : bond 0.00356 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 2.392 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: A 95 MET cc_start: 0.8596 (ppp) cc_final: 0.8290 (ppp) REVERT: A 96 TRP cc_start: 0.8689 (m-90) cc_final: 0.7885 (m-90) REVERT: A 104 MET cc_start: 0.8802 (tpp) cc_final: 0.8363 (tpt) REVERT: A 217 TYR cc_start: 0.8099 (m-80) cc_final: 0.7374 (m-80) REVERT: A 426 MET cc_start: 0.8248 (tpp) cc_final: 0.8015 (tpp) REVERT: B 587 LEU cc_start: 0.9654 (mt) cc_final: 0.9367 (tp) REVERT: B 629 MET cc_start: 0.8138 (tpp) cc_final: 0.7741 (tpp) REVERT: C 297 THR cc_start: 0.8446 (p) cc_final: 0.8098 (p) REVERT: C 373 MET cc_start: 0.8735 (mmm) cc_final: 0.8444 (mmt) REVERT: C 482 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8585 (mm-30) REVERT: D 530 MET cc_start: 0.7955 (mtm) cc_final: 0.7386 (mpp) REVERT: D 540 GLN cc_start: 0.7999 (mp10) cc_final: 0.7574 (mp10) REVERT: D 559 ILE cc_start: 0.8997 (mt) cc_final: 0.8725 (mt) REVERT: D 565 MET cc_start: 0.8063 (tpt) cc_final: 0.7750 (tmm) REVERT: D 626 MET cc_start: 0.8914 (tpp) cc_final: 0.8059 (mmm) REVERT: D 636 ASP cc_start: 0.8766 (t0) cc_final: 0.8546 (t0) REVERT: D 647 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7685 (mp0) REVERT: E 42 VAL cc_start: 0.9594 (t) cc_final: 0.9386 (p) REVERT: E 475 MET cc_start: 0.8284 (mpp) cc_final: 0.7909 (mpp) REVERT: E 505 VAL cc_start: 0.8372 (p) cc_final: 0.8133 (p) REVERT: H 45 LEU cc_start: 0.8885 (mt) cc_final: 0.8675 (mt) REVERT: H 67 PHE cc_start: 0.8268 (m-80) cc_final: 0.7986 (m-80) REVERT: H 72 ASP cc_start: 0.7948 (t0) cc_final: 0.7520 (t70) REVERT: H 77 THR cc_start: 0.8039 (p) cc_final: 0.7302 (p) REVERT: H 79 TYR cc_start: 0.8198 (m-80) cc_final: 0.7307 (m-10) REVERT: H 100 MET cc_start: 0.8048 (pmm) cc_final: 0.7751 (pmm) REVERT: L 36 TYR cc_start: 0.8135 (m-80) cc_final: 0.6958 (m-80) REVERT: L 77 ARG cc_start: 0.8435 (ptp90) cc_final: 0.8185 (ptt180) REVERT: M 100 MET cc_start: 0.9078 (mpp) cc_final: 0.8863 (mpp) REVERT: N 13 VAL cc_start: 0.8501 (m) cc_final: 0.8290 (m) REVERT: N 45 GLN cc_start: 0.8456 (mm110) cc_final: 0.8164 (mp10) outliers start: 2 outliers final: 1 residues processed: 284 average time/residue: 0.3326 time to fit residues: 148.1774 Evaluate side-chains 195 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 14 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061295 restraints weight = 67806.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063078 restraints weight = 40709.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.064303 restraints weight = 29551.677| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21349 Z= 0.153 Angle : 0.874 25.004 29337 Z= 0.392 Chirality : 0.051 0.465 3850 Planarity : 0.004 0.044 3338 Dihedral : 9.539 62.553 6745 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.20 % Favored : 93.40 % Rotamer: Outliers : 0.10 % Allowed : 0.80 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2243 helix: 0.14 (0.25), residues: 435 sheet: -0.53 (0.20), residues: 599 loop : -1.26 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.002 TRP E 45 HIS 0.007 0.001 HIS C 330 PHE 0.029 0.002 PHE H 29 TYR 0.036 0.001 TYR H 32 ARG 0.017 0.001 ARG B 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 64) link_NAG-ASN : angle 3.41428 ( 192) link_ALPHA1-6 : bond 0.00898 ( 14) link_ALPHA1-6 : angle 1.85213 ( 42) link_BETA1-2 : bond 0.00267 ( 8) link_BETA1-2 : angle 1.84917 ( 24) link_BETA1-4 : bond 0.00383 ( 96) link_BETA1-4 : angle 2.06193 ( 288) link_ALPHA1-2 : bond 0.00753 ( 6) link_ALPHA1-2 : angle 1.75236 ( 18) link_ALPHA1-3 : bond 0.01141 ( 16) link_ALPHA1-3 : angle 1.66541 ( 48) hydrogen bonds : bond 0.04277 ( 688) hydrogen bonds : angle 5.59894 ( 2016) link_BETA1-6 : bond 0.00261 ( 9) link_BETA1-6 : angle 1.31512 ( 27) SS BOND : bond 0.00307 ( 34) SS BOND : angle 1.56480 ( 68) covalent geometry : bond 0.00320 (21101) covalent geometry : angle 0.79956 (28630) Misc. bond : bond 0.00282 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 288 time to evaluate : 2.347 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: A 104 MET cc_start: 0.8884 (tpp) cc_final: 0.8508 (tpt) REVERT: A 217 TYR cc_start: 0.8143 (m-80) cc_final: 0.7427 (m-80) REVERT: A 484 TYR cc_start: 0.8800 (p90) cc_final: 0.8585 (p90) REVERT: B 557 ARG cc_start: 0.8734 (mpp-170) cc_final: 0.8348 (mtm-85) REVERT: B 587 LEU cc_start: 0.9598 (mt) cc_final: 0.9305 (tp) REVERT: B 651 ASN cc_start: 0.8129 (m110) cc_final: 0.7897 (m110) REVERT: C 95 MET cc_start: 0.8918 (ptm) cc_final: 0.8658 (ptm) REVERT: C 100 MET cc_start: 0.8479 (mtm) cc_final: 0.8086 (mtm) REVERT: C 297 THR cc_start: 0.8258 (p) cc_final: 0.7904 (p) REVERT: C 373 MET cc_start: 0.8651 (mmm) cc_final: 0.8321 (mmm) REVERT: C 482 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8487 (mm-30) REVERT: D 530 MET cc_start: 0.7758 (mtm) cc_final: 0.7126 (mpp) REVERT: D 536 THR cc_start: 0.8627 (p) cc_final: 0.7263 (p) REVERT: D 540 GLN cc_start: 0.8075 (mp10) cc_final: 0.7634 (mp10) REVERT: D 559 ILE cc_start: 0.8964 (mt) cc_final: 0.8678 (mt) REVERT: D 626 MET cc_start: 0.8947 (tpp) cc_final: 0.7797 (tmm) REVERT: D 647 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7566 (mp0) REVERT: E 434 MET cc_start: 0.8533 (ptt) cc_final: 0.8294 (ptm) REVERT: F 534 SER cc_start: 0.9054 (p) cc_final: 0.8455 (p) REVERT: F 535 MET cc_start: 0.8248 (mpp) cc_final: 0.7923 (mpp) REVERT: F 536 THR cc_start: 0.8642 (m) cc_final: 0.8239 (p) REVERT: F 629 MET cc_start: 0.7870 (mtt) cc_final: 0.7216 (mtt) REVERT: F 654 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7900 (tp30) REVERT: H 45 LEU cc_start: 0.8891 (mt) cc_final: 0.8576 (mt) REVERT: H 72 ASP cc_start: 0.7925 (t0) cc_final: 0.7643 (t0) REVERT: H 77 THR cc_start: 0.8019 (p) cc_final: 0.7203 (p) REVERT: H 79 TYR cc_start: 0.8071 (m-80) cc_final: 0.7246 (m-10) REVERT: H 100 MET cc_start: 0.8008 (pmm) cc_final: 0.7663 (pmm) REVERT: L 14 THR cc_start: 0.7926 (p) cc_final: 0.7700 (p) REVERT: L 77 ARG cc_start: 0.8407 (ptp90) cc_final: 0.8171 (ptt180) REVERT: M 95 MET cc_start: 0.8387 (ttm) cc_final: 0.8139 (ttp) REVERT: M 100 TYR cc_start: 0.8006 (m-80) cc_final: 0.7362 (m-10) REVERT: M 100 MET cc_start: 0.9068 (mpp) cc_final: 0.8609 (mpp) REVERT: N 27 GLU cc_start: 0.8536 (tp30) cc_final: 0.8059 (tp30) outliers start: 2 outliers final: 2 residues processed: 290 average time/residue: 0.3102 time to fit residues: 142.8062 Evaluate side-chains 207 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 8 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 78 optimal weight: 0.0070 chunk 64 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 577 GLN C 302 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN H 76 ASN M 76 ASN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 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 = 0.3391 r_free = 0.3391 target = 0.081058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.062700 restraints weight = 67804.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064518 restraints weight = 40590.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065745 restraints weight = 29254.309| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21349 Z= 0.135 Angle : 0.861 30.421 29337 Z= 0.385 Chirality : 0.050 0.459 3850 Planarity : 0.004 0.069 3338 Dihedral : 8.924 59.229 6745 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.93 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.04 (0.17), residues: 2243 helix: 0.24 (0.25), residues: 436 sheet: -0.37 (0.20), residues: 593 loop : -1.18 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP E 45 HIS 0.006 0.001 HIS C 330 PHE 0.011 0.001 PHE H 27 TYR 0.012 0.001 TYR D 638 ARG 0.010 0.000 ARG B 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 64) link_NAG-ASN : angle 3.17141 ( 192) link_ALPHA1-6 : bond 0.00922 ( 14) link_ALPHA1-6 : angle 1.83441 ( 42) link_BETA1-2 : bond 0.00247 ( 8) link_BETA1-2 : angle 1.76294 ( 24) link_BETA1-4 : bond 0.00411 ( 96) link_BETA1-4 : angle 1.94266 ( 288) link_ALPHA1-2 : bond 0.00785 ( 6) link_ALPHA1-2 : angle 1.77069 ( 18) link_ALPHA1-3 : bond 0.01161 ( 16) link_ALPHA1-3 : angle 1.57315 ( 48) hydrogen bonds : bond 0.04027 ( 688) hydrogen bonds : angle 5.40420 ( 2016) link_BETA1-6 : bond 0.00403 ( 9) link_BETA1-6 : angle 1.15282 ( 27) SS BOND : bond 0.00285 ( 34) SS BOND : angle 2.07002 ( 68) covalent geometry : bond 0.00275 (21101) covalent geometry : angle 0.79345 (28630) Misc. bond : bond 0.00239 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 2.065 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: A 104 MET cc_start: 0.8742 (tpp) cc_final: 0.8224 (tpp) REVERT: A 217 TYR cc_start: 0.7931 (m-80) cc_final: 0.7403 (m-80) REVERT: A 484 TYR cc_start: 0.8778 (p90) cc_final: 0.8532 (p90) REVERT: B 530 MET cc_start: 0.7969 (mmp) cc_final: 0.7636 (mmp) REVERT: B 554 ASN cc_start: 0.7921 (t0) cc_final: 0.7184 (t0) REVERT: B 557 ARG cc_start: 0.8675 (mpp-170) cc_final: 0.8435 (mpp-170) REVERT: B 587 LEU cc_start: 0.9556 (mt) cc_final: 0.9282 (tp) REVERT: C 95 MET cc_start: 0.8902 (ptm) cc_final: 0.8675 (ptm) REVERT: C 100 MET cc_start: 0.8522 (mtm) cc_final: 0.8081 (mtm) REVERT: C 297 THR cc_start: 0.8070 (p) cc_final: 0.7820 (p) REVERT: C 373 MET cc_start: 0.8539 (mmm) cc_final: 0.8254 (mmm) REVERT: C 482 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8456 (mm-30) REVERT: D 530 MET cc_start: 0.7716 (mtm) cc_final: 0.7306 (mpp) REVERT: D 536 THR cc_start: 0.8378 (p) cc_final: 0.7094 (p) REVERT: D 540 GLN cc_start: 0.8018 (mp10) cc_final: 0.7761 (mp10) REVERT: D 559 ILE cc_start: 0.9007 (mt) cc_final: 0.8742 (mt) REVERT: D 626 MET cc_start: 0.8849 (tpp) cc_final: 0.8035 (tmm) REVERT: D 647 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7602 (mp0) REVERT: E 42 VAL cc_start: 0.9522 (t) cc_final: 0.9281 (p) REVERT: E 104 MET cc_start: 0.9321 (ttt) cc_final: 0.9071 (ttt) REVERT: E 318 TYR cc_start: 0.8257 (m-80) cc_final: 0.7894 (m-80) REVERT: E 434 MET cc_start: 0.8634 (ptt) cc_final: 0.8301 (ptt) REVERT: E 484 TYR cc_start: 0.8911 (p90) cc_final: 0.8267 (p90) REVERT: F 534 SER cc_start: 0.8950 (p) cc_final: 0.8048 (p) REVERT: F 536 THR cc_start: 0.8346 (m) cc_final: 0.8009 (p) REVERT: F 626 MET cc_start: 0.8989 (tpp) cc_final: 0.8765 (mmm) REVERT: F 654 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7519 (tp30) REVERT: H 45 LEU cc_start: 0.8836 (mt) cc_final: 0.8403 (mt) REVERT: H 67 PHE cc_start: 0.7868 (m-80) cc_final: 0.6993 (m-80) REVERT: H 72 ASP cc_start: 0.7877 (t0) cc_final: 0.7400 (t70) REVERT: H 77 THR cc_start: 0.8005 (p) cc_final: 0.7239 (p) REVERT: H 79 TYR cc_start: 0.8084 (m-80) cc_final: 0.7284 (m-10) REVERT: H 82 MET cc_start: 0.7779 (mtt) cc_final: 0.7115 (mtt) REVERT: H 100 MET cc_start: 0.7811 (pmm) cc_final: 0.7552 (pmm) REVERT: L 36 TYR cc_start: 0.8196 (m-80) cc_final: 0.6780 (m-80) REVERT: L 73 LEU cc_start: 0.8501 (tp) cc_final: 0.7690 (tp) REVERT: M 95 MET cc_start: 0.8303 (ttm) cc_final: 0.7510 (ttp) REVERT: M 100 MET cc_start: 0.9057 (mpp) cc_final: 0.8572 (mpp) REVERT: N 4 MET cc_start: 0.6944 (mmp) cc_final: 0.6623 (tpp) REVERT: N 27 GLU cc_start: 0.8510 (tp30) cc_final: 0.8002 (tp30) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2760 time to fit residues: 134.8537 Evaluate side-chains 214 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 107 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 197 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 174 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 577 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN H 73 ASN M 76 ASN M 97 GLN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 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 = 0.3367 r_free = 0.3367 target = 0.079764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.061531 restraints weight = 68756.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063220 restraints weight = 42399.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064366 restraints weight = 31191.542| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21349 Z= 0.170 Angle : 0.874 27.834 29337 Z= 0.392 Chirality : 0.050 0.467 3850 Planarity : 0.004 0.061 3338 Dihedral : 8.753 59.807 6745 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.73 % Favored : 92.91 % Rotamer: Outliers : 0.05 % Allowed : 1.10 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.17), residues: 2243 helix: 0.20 (0.25), residues: 438 sheet: -0.41 (0.20), residues: 613 loop : -1.15 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP E 45 HIS 0.007 0.001 HIS C 330 PHE 0.013 0.002 PHE M 67 TYR 0.012 0.001 TYR H 32 ARG 0.009 0.001 ARG B 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 64) link_NAG-ASN : angle 3.27320 ( 192) link_ALPHA1-6 : bond 0.00874 ( 14) link_ALPHA1-6 : angle 1.85342 ( 42) link_BETA1-2 : bond 0.00306 ( 8) link_BETA1-2 : angle 1.83475 ( 24) link_BETA1-4 : bond 0.00352 ( 96) link_BETA1-4 : angle 1.95584 ( 288) link_ALPHA1-2 : bond 0.00740 ( 6) link_ALPHA1-2 : angle 1.67477 ( 18) link_ALPHA1-3 : bond 0.01125 ( 16) link_ALPHA1-3 : angle 1.58492 ( 48) hydrogen bonds : bond 0.04162 ( 688) hydrogen bonds : angle 5.35614 ( 2016) link_BETA1-6 : bond 0.00319 ( 9) link_BETA1-6 : angle 1.51779 ( 27) SS BOND : bond 0.00272 ( 34) SS BOND : angle 2.19788 ( 68) covalent geometry : bond 0.00369 (21101) covalent geometry : angle 0.80344 (28630) Misc. bond : bond 0.00271 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 2.023 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: A 104 MET cc_start: 0.8742 (tpp) cc_final: 0.8133 (tpp) REVERT: A 217 TYR cc_start: 0.7865 (m-80) cc_final: 0.7381 (m-80) REVERT: A 484 TYR cc_start: 0.8829 (p90) cc_final: 0.8542 (p90) REVERT: B 554 ASN cc_start: 0.7936 (t0) cc_final: 0.6995 (t0) REVERT: B 557 ARG cc_start: 0.8765 (mpp-170) cc_final: 0.8330 (mpp-170) REVERT: B 587 LEU cc_start: 0.9603 (mt) cc_final: 0.9313 (tp) REVERT: C 95 MET cc_start: 0.8897 (ptm) cc_final: 0.8665 (ptm) REVERT: C 297 THR cc_start: 0.8060 (p) cc_final: 0.7763 (p) REVERT: C 373 MET cc_start: 0.8562 (mmm) cc_final: 0.8303 (mmt) REVERT: C 482 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8462 (mm-30) REVERT: D 536 THR cc_start: 0.8474 (p) cc_final: 0.7125 (p) REVERT: D 540 GLN cc_start: 0.8099 (mp10) cc_final: 0.7721 (mp10) REVERT: D 565 MET cc_start: 0.7954 (tpt) cc_final: 0.7499 (tmm) REVERT: D 647 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7610 (mp0) REVERT: E 42 VAL cc_start: 0.9506 (t) cc_final: 0.9195 (p) REVERT: E 104 MET cc_start: 0.9336 (ttt) cc_final: 0.9057 (ttt) REVERT: E 318 TYR cc_start: 0.8273 (m-80) cc_final: 0.7933 (m-80) REVERT: E 434 MET cc_start: 0.8730 (ptt) cc_final: 0.8487 (ptt) REVERT: E 484 TYR cc_start: 0.8834 (p90) cc_final: 0.8323 (p90) REVERT: F 536 THR cc_start: 0.8439 (m) cc_final: 0.8109 (p) REVERT: F 654 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7760 (mm-30) REVERT: H 45 LEU cc_start: 0.8797 (mt) cc_final: 0.8369 (mt) REVERT: H 72 ASP cc_start: 0.7948 (t0) cc_final: 0.7561 (t70) REVERT: H 77 THR cc_start: 0.7760 (p) cc_final: 0.6973 (p) REVERT: H 79 TYR cc_start: 0.8224 (m-80) cc_final: 0.7386 (m-10) REVERT: H 82 MET cc_start: 0.7817 (mtt) cc_final: 0.7231 (mtt) REVERT: H 100 MET cc_start: 0.7805 (pmm) cc_final: 0.7468 (pmm) REVERT: L 27 LEU cc_start: 0.8772 (mt) cc_final: 0.8480 (mp) REVERT: L 36 TYR cc_start: 0.8253 (m-80) cc_final: 0.6979 (m-80) REVERT: M 35 TYR cc_start: 0.8393 (m-10) cc_final: 0.7973 (m-10) REVERT: M 67 PHE cc_start: 0.8298 (m-10) cc_final: 0.8004 (m-10) REVERT: M 82 MET cc_start: 0.8826 (mmm) cc_final: 0.8468 (mmm) REVERT: M 95 MET cc_start: 0.8408 (ttm) cc_final: 0.7851 (ttp) REVERT: M 100 MET cc_start: 0.9080 (mpp) cc_final: 0.8688 (mpp) REVERT: N 27 GLU cc_start: 0.8549 (tp30) cc_final: 0.8095 (tp30) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.2850 time to fit residues: 129.5939 Evaluate side-chains 206 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 GLN M 76 ASN M 97 GLN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.060974 restraints weight = 68913.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062639 restraints weight = 42274.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.063763 restraints weight = 31141.239| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21349 Z= 0.183 Angle : 0.891 24.975 29337 Z= 0.401 Chirality : 0.051 0.469 3850 Planarity : 0.004 0.057 3338 Dihedral : 8.693 59.948 6745 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.60 % Favored : 93.00 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.09 (0.17), residues: 2243 helix: -0.00 (0.25), residues: 449 sheet: -0.37 (0.20), residues: 614 loop : -1.17 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP E 45 HIS 0.007 0.001 HIS C 330 PHE 0.018 0.002 PHE H 27 TYR 0.015 0.001 TYR H 32 ARG 0.012 0.001 ARG B 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 64) link_NAG-ASN : angle 3.31966 ( 192) link_ALPHA1-6 : bond 0.00858 ( 14) link_ALPHA1-6 : angle 1.83960 ( 42) link_BETA1-2 : bond 0.00307 ( 8) link_BETA1-2 : angle 1.78285 ( 24) link_BETA1-4 : bond 0.00365 ( 96) link_BETA1-4 : angle 1.91486 ( 288) link_ALPHA1-2 : bond 0.00724 ( 6) link_ALPHA1-2 : angle 1.72245 ( 18) link_ALPHA1-3 : bond 0.01143 ( 16) link_ALPHA1-3 : angle 1.61366 ( 48) hydrogen bonds : bond 0.04279 ( 688) hydrogen bonds : angle 5.46080 ( 2016) link_BETA1-6 : bond 0.00314 ( 9) link_BETA1-6 : angle 1.52038 ( 27) SS BOND : bond 0.00359 ( 34) SS BOND : angle 2.31970 ( 68) covalent geometry : bond 0.00401 (21101) covalent geometry : angle 0.82072 (28630) Misc. bond : bond 0.00261 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 2.337 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: A 104 MET cc_start: 0.8877 (tpp) cc_final: 0.8576 (tpt) REVERT: A 217 TYR cc_start: 0.7988 (m-80) cc_final: 0.7530 (m-80) REVERT: A 484 TYR cc_start: 0.8835 (p90) cc_final: 0.8526 (p90) REVERT: B 565 MET cc_start: 0.7341 (mtm) cc_final: 0.6320 (tmm) REVERT: B 587 LEU cc_start: 0.9623 (mt) cc_final: 0.9379 (tp) REVERT: C 95 MET cc_start: 0.8924 (ptm) cc_final: 0.8683 (ptm) REVERT: C 100 MET cc_start: 0.8324 (mtm) cc_final: 0.8025 (mtt) REVERT: C 297 THR cc_start: 0.8040 (p) cc_final: 0.7728 (p) REVERT: C 373 MET cc_start: 0.8569 (mmm) cc_final: 0.8310 (mmt) REVERT: C 482 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8477 (mm-30) REVERT: D 530 MET cc_start: 0.7735 (mtp) cc_final: 0.7412 (ttm) REVERT: D 565 MET cc_start: 0.8143 (tpt) cc_final: 0.7545 (tmm) REVERT: D 626 MET cc_start: 0.8695 (tpt) cc_final: 0.8457 (mmm) REVERT: E 104 MET cc_start: 0.9316 (ttt) cc_final: 0.9065 (ttt) REVERT: E 191 TYR cc_start: 0.8267 (m-80) cc_final: 0.7983 (m-80) REVERT: E 318 TYR cc_start: 0.8297 (m-80) cc_final: 0.8020 (m-80) REVERT: E 434 MET cc_start: 0.8693 (ptt) cc_final: 0.8085 (ptt) REVERT: E 484 TYR cc_start: 0.8908 (p90) cc_final: 0.8215 (p90) REVERT: F 536 THR cc_start: 0.8534 (m) cc_final: 0.8276 (p) REVERT: F 654 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7675 (mm-30) REVERT: H 31 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7781 (ptmm) REVERT: H 45 LEU cc_start: 0.8832 (mt) cc_final: 0.8394 (mt) REVERT: H 77 THR cc_start: 0.7718 (p) cc_final: 0.6895 (p) REVERT: H 79 TYR cc_start: 0.8239 (m-80) cc_final: 0.7403 (m-10) REVERT: H 100 MET cc_start: 0.7887 (pmm) cc_final: 0.7504 (pmm) REVERT: L 27 LEU cc_start: 0.8765 (mt) cc_final: 0.8488 (mp) REVERT: L 36 TYR cc_start: 0.8305 (m-80) cc_final: 0.6881 (m-80) REVERT: L 74 ARG cc_start: 0.8321 (tmt-80) cc_final: 0.7887 (tpt90) REVERT: L 79 GLU cc_start: 0.7293 (tt0) cc_final: 0.6793 (tm-30) REVERT: M 67 PHE cc_start: 0.8325 (m-10) cc_final: 0.7913 (m-10) REVERT: M 82 MET cc_start: 0.8760 (mmm) cc_final: 0.8484 (mmm) REVERT: M 95 MET cc_start: 0.8520 (ttm) cc_final: 0.7891 (ttp) REVERT: M 100 MET cc_start: 0.9081 (mpp) cc_final: 0.8802 (mpp) REVERT: N 4 MET cc_start: 0.6926 (mmp) cc_final: 0.6389 (tpp) REVERT: N 27 GLU cc_start: 0.8526 (tp30) cc_final: 0.8102 (tp30) REVERT: N 81 GLU cc_start: 0.7840 (pm20) cc_final: 0.7576 (pm20) REVERT: N 105 ASP cc_start: 0.7745 (p0) cc_final: 0.7381 (p0) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2974 time to fit residues: 130.0201 Evaluate side-chains 200 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 9.9990 chunk 204 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN H 39 GLN H 76 ASN M 97 GLN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 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 = 0.3374 r_free = 0.3374 target = 0.080080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061950 restraints weight = 67484.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.063730 restraints weight = 40369.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.064916 restraints weight = 29153.486| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21349 Z= 0.145 Angle : 0.856 27.881 29337 Z= 0.385 Chirality : 0.050 0.456 3850 Planarity : 0.004 0.055 3338 Dihedral : 8.399 56.161 6745 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.78 % Favored : 92.87 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.18), residues: 2243 helix: 0.21 (0.25), residues: 438 sheet: -0.35 (0.20), residues: 638 loop : -1.19 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP E 45 HIS 0.011 0.001 HIS A 374 PHE 0.012 0.001 PHE L 55 TYR 0.021 0.001 TYR M 79 ARG 0.013 0.000 ARG B 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 64) link_NAG-ASN : angle 3.17703 ( 192) link_ALPHA1-6 : bond 0.00890 ( 14) link_ALPHA1-6 : angle 1.78899 ( 42) link_BETA1-2 : bond 0.00212 ( 8) link_BETA1-2 : angle 1.68491 ( 24) link_BETA1-4 : bond 0.00382 ( 96) link_BETA1-4 : angle 1.84540 ( 288) link_ALPHA1-2 : bond 0.00754 ( 6) link_ALPHA1-2 : angle 1.79728 ( 18) link_ALPHA1-3 : bond 0.01107 ( 16) link_ALPHA1-3 : angle 1.55649 ( 48) hydrogen bonds : bond 0.04084 ( 688) hydrogen bonds : angle 5.34870 ( 2016) link_BETA1-6 : bond 0.00284 ( 9) link_BETA1-6 : angle 1.33553 ( 27) SS BOND : bond 0.00523 ( 34) SS BOND : angle 2.35574 ( 68) covalent geometry : bond 0.00308 (21101) covalent geometry : angle 0.78758 (28630) Misc. bond : bond 0.00231 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 2.077 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: A 104 MET cc_start: 0.8776 (tpp) cc_final: 0.8478 (tpp) REVERT: A 217 TYR cc_start: 0.7793 (m-80) cc_final: 0.7397 (m-80) REVERT: A 484 TYR cc_start: 0.8811 (p90) cc_final: 0.8504 (p90) REVERT: B 587 LEU cc_start: 0.9591 (mt) cc_final: 0.9336 (tp) REVERT: C 95 MET cc_start: 0.8968 (ptm) cc_final: 0.8709 (ptm) REVERT: C 100 MET cc_start: 0.8371 (mtm) cc_final: 0.8039 (mtt) REVERT: C 297 THR cc_start: 0.8061 (p) cc_final: 0.7790 (p) REVERT: C 373 MET cc_start: 0.8530 (mmm) cc_final: 0.8254 (mmm) REVERT: C 482 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8477 (mm-30) REVERT: D 530 MET cc_start: 0.7798 (mtp) cc_final: 0.7357 (ttm) REVERT: D 536 THR cc_start: 0.8484 (p) cc_final: 0.7029 (p) REVERT: D 540 GLN cc_start: 0.8098 (mp10) cc_final: 0.7601 (mp10) REVERT: D 634 GLU cc_start: 0.9020 (tt0) cc_final: 0.8805 (tt0) REVERT: E 191 TYR cc_start: 0.8307 (m-80) cc_final: 0.8017 (m-80) REVERT: E 318 TYR cc_start: 0.8311 (m-80) cc_final: 0.8002 (m-80) REVERT: E 434 MET cc_start: 0.8747 (ptt) cc_final: 0.8305 (ptt) REVERT: F 536 THR cc_start: 0.8403 (m) cc_final: 0.8093 (p) REVERT: F 591 GLN cc_start: 0.8731 (tt0) cc_final: 0.8457 (tp-100) REVERT: F 629 MET cc_start: 0.8348 (mtm) cc_final: 0.8103 (mtt) REVERT: H 31 LYS cc_start: 0.8067 (ptmt) cc_final: 0.7737 (ptmm) REVERT: H 45 LEU cc_start: 0.8840 (mt) cc_final: 0.8325 (mt) REVERT: H 77 THR cc_start: 0.7872 (p) cc_final: 0.7058 (p) REVERT: H 79 TYR cc_start: 0.8269 (m-80) cc_final: 0.7443 (m-10) REVERT: H 100 MET cc_start: 0.7891 (pmm) cc_final: 0.7491 (pmm) REVERT: L 27 LEU cc_start: 0.8743 (mt) cc_final: 0.8481 (mp) REVERT: L 36 TYR cc_start: 0.8267 (m-80) cc_final: 0.6964 (m-80) REVERT: L 79 GLU cc_start: 0.7317 (tt0) cc_final: 0.6857 (tm-30) REVERT: M 82 MET cc_start: 0.8638 (mmm) cc_final: 0.8397 (mmm) REVERT: M 100 MET cc_start: 0.9103 (mpp) cc_final: 0.8866 (mpp) REVERT: N 4 MET cc_start: 0.6942 (mmp) cc_final: 0.6396 (tpp) REVERT: N 27 GLU cc_start: 0.8625 (tp30) cc_final: 0.8141 (tp30) REVERT: N 81 GLU cc_start: 0.7852 (pm20) cc_final: 0.7617 (pm20) REVERT: N 105 ASP cc_start: 0.7839 (p0) cc_final: 0.7477 (p0) outliers start: 1 outliers final: 0 residues processed: 268 average time/residue: 0.3197 time to fit residues: 138.5761 Evaluate side-chains 200 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 137 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 57 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.3520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN H 76 ASN M 97 GLN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.062490 restraints weight = 69478.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064183 restraints weight = 42922.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065315 restraints weight = 31597.761| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21349 Z= 0.149 Angle : 0.849 26.217 29337 Z= 0.383 Chirality : 0.050 0.455 3850 Planarity : 0.004 0.055 3338 Dihedral : 8.244 56.398 6745 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.55 % Favored : 93.00 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2243 helix: 0.23 (0.25), residues: 436 sheet: -0.24 (0.20), residues: 604 loop : -1.18 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 45 HIS 0.007 0.001 HIS A 374 PHE 0.012 0.001 PHE N 98 TYR 0.026 0.001 TYR M 79 ARG 0.011 0.000 ARG B 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 64) link_NAG-ASN : angle 3.09881 ( 192) link_ALPHA1-6 : bond 0.00873 ( 14) link_ALPHA1-6 : angle 1.77969 ( 42) link_BETA1-2 : bond 0.00235 ( 8) link_BETA1-2 : angle 1.69169 ( 24) link_BETA1-4 : bond 0.00368 ( 96) link_BETA1-4 : angle 1.82967 ( 288) link_ALPHA1-2 : bond 0.00744 ( 6) link_ALPHA1-2 : angle 1.78187 ( 18) link_ALPHA1-3 : bond 0.01109 ( 16) link_ALPHA1-3 : angle 1.53960 ( 48) hydrogen bonds : bond 0.04067 ( 688) hydrogen bonds : angle 5.35479 ( 2016) link_BETA1-6 : bond 0.00282 ( 9) link_BETA1-6 : angle 1.40652 ( 27) SS BOND : bond 0.00319 ( 34) SS BOND : angle 2.19456 ( 68) covalent geometry : bond 0.00322 (21101) covalent geometry : angle 0.78411 (28630) Misc. bond : bond 0.00236 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5987.58 seconds wall clock time: 105 minutes 32.58 seconds (6332.58 seconds total)