Starting phenix.real_space_refine on Sun Sep 29 08:39:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tox_41461/09_2024/8tox_41461.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tox_41461/09_2024/8tox_41461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tox_41461/09_2024/8tox_41461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tox_41461/09_2024/8tox_41461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tox_41461/09_2024/8tox_41461.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tox_41461/09_2024/8tox_41461.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 132 5.16 5 C 13533 2.51 5 N 3528 2.21 5 O 4815 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-5461/modules/chem_data/mon_lib" Total number of atoms: 22008 Number of models: 1 Model: "" Number of chains: 78 Chain: "B" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1094 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "G" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3559 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "A" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1094 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "C" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3559 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "F" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1094 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3559 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1029 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1029 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1029 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: "m" 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: "n" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: 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: "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: 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: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "3" 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 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: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" 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: "B" 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: "G" 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: "A" 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: "C" 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: "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 Chain: "I" 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "I" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 14.85, per 1000 atoms: 0.67 Number of scatterers: 22008 At special positions: 0 Unit cell: (151.89, 158.53, 131.14, 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 132 16.00 O 4815 8.00 N 3528 7.00 C 13533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.02 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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 D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 2 4 " - " MAN 2 5 " " MAN U 4 " - " MAN U 5 " " MAN l 4 " - " MAN l 5 " ALPHA1-3 " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 4 " " BMA O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 4 " " BMA l 3 " - " MAN l 4 " " BMA m 3 " - " MAN m 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA 2 3 " - " MAN 2 6 " " BMA 3 3 " - " MAN 3 5 " " BMA O 3 " - " MAN O 5 " " BMA U 3 " - " MAN U 6 " " BMA V 3 " - " MAN V 5 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 5 " " BMA l 3 " - " MAN l 6 " " BMA m 3 " - " MAN m 5 " " BMA t 3 " - " MAN t 5 " " BMA w 3 " - " MAN w 5 " " BMAAA 3 " - " MANAA 5 " 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 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " 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 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 z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN I 234 " " NAG 1 1 " - " ASN I 241 " " NAG 2 1 " - " ASN I 262 " " NAG 3 1 " - " ASN I 276 " " NAG 4 1 " - " ASN I 295 " " NAG 5 1 " - " ASN I 301 " " NAG 6 1 " - " ASN I 355 " " NAG 7 1 " - " ASN I 386 " " NAG 8 1 " - " ASN I 392 " " NAG 9 1 " - " ASN I 448 " " NAG A 701 " - " ASN A 618 " " NAG B 701 " - " ASN B 618 " " NAG C 601 " - " ASN C 137 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 363 " " NAG F 701 " - " ASN F 618 " " NAG G 601 " - " ASN G 137 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 363 " " NAG I 601 " - " ASN I 137 " " NAG I 602 " - " ASN I 339 " " NAG I 603 " - " ASN I 363 " " NAG M 1 " - " ASN B 611 " " NAG N 1 " - " ASN B 637 " " NAG O 1 " - " ASN G 88 " " NAG P 1 " - " ASN G 133 " " NAG Q 1 " - " ASN G 160 " " NAG R 1 " - " ASN G 197 " " NAG S 1 " - " ASN G 234 " " NAG T 1 " - " ASN G 241 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 276 " " NAG W 1 " - " ASN G 295 " " NAG X 1 " - " ASN G 301 " " NAG Y 1 " - " ASN G 355 " " NAG Z 1 " - " ASN G 386 " " NAG a 1 " - " ASN G 392 " " NAG b 1 " - " ASN G 448 " " NAG c 1 " - " ASN G 156 " " NAG d 1 " - " ASN A 611 " " NAG e 1 " - " ASN A 637 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN C 133 " " NAG h 1 " - " ASN C 160 " " NAG i 1 " - " ASN C 197 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 241 " " NAG l 1 " - " ASN C 262 " " NAG m 1 " - " ASN C 276 " " NAG n 1 " - " ASN C 295 " " NAG o 1 " - " ASN C 301 " " NAG p 1 " - " ASN C 355 " " NAG q 1 " - " ASN C 386 " " NAG r 1 " - " ASN C 392 " " NAG s 1 " - " ASN C 448 " " NAG t 1 " - " ASN C 156 " " NAG u 1 " - " ASN F 611 " " NAG v 1 " - " ASN F 637 " " NAG w 1 " - " ASN I 88 " " NAG x 1 " - " ASN I 133 " " NAG y 1 " - " ASN I 160 " " NAG z 1 " - " ASN I 197 " " NAGAA 1 " - " ASN I 156 " Time building additional restraints: 7.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4566 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 23.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.568A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 4.281A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.672A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'G' and resid 57 through 64 removed outlier: 4.269A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 73 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.059A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 334 through 354 removed outlier: 3.791A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 458 through 462 removed outlier: 4.430A pdb=" N THR G 461 " --> pdb=" O GLY G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.840A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.568A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 4.281A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.672A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 663 Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.270A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.060A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.791A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 458 through 462 removed outlier: 4.430A pdb=" N THR C 461 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.840A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.567A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 547 removed outlier: 4.281A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.672A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'I' and resid 57 through 64 removed outlier: 4.269A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 73 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.059A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.792A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 458 through 462 removed outlier: 4.431A pdb=" N THR I 461 " --> pdb=" O GLY I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 3.840A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.697A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.891A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.697A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.891A pdb=" N VAL E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.697A pdb=" N THR J 87 " --> pdb=" O THR J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.891A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 513 through 515 Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.363A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.973A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.141A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 260 through 261 current: chain 'G' and resid 284 through 312 removed outlier: 6.727A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 323 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.353A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.973A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.141A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.726A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'F' and resid 513 through 515 Processing sheet with id=AB9, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.350A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.973A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.141A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 261 current: chain 'I' and resid 284 through 312 removed outlier: 6.726A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.773A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.157A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 12 current: chain 'D' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 59 current: chain 'D' and resid 102 through 103 Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.773A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.157A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU E 33 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N HIS E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 102 through 103 Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.772A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.157A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1764 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: 8.55 Time building geometry restraints manager: 8.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3345 1.30 - 1.43: 5993 1.43 - 1.56: 12541 1.56 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 22059 Sorted by residual: bond pdb=" C HIS C 216 " pdb=" O HIS C 216 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.21e-02 6.83e+03 2.35e+01 bond pdb=" C HIS G 216 " pdb=" O HIS G 216 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.21e-02 6.83e+03 2.34e+01 bond pdb=" C HIS I 216 " pdb=" O HIS I 216 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.21e-02 6.83e+03 2.29e+01 bond pdb=" C ASN C 156 " pdb=" N CYS C 157 " ideal model delta sigma weight residual 1.330 1.274 0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" C ASN G 156 " pdb=" N CYS G 157 " ideal model delta sigma weight residual 1.330 1.275 0.055 1.40e-02 5.10e+03 1.54e+01 ... (remaining 22054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 27893 1.29 - 2.58: 1460 2.58 - 3.87: 346 3.87 - 5.16: 129 5.16 - 6.46: 79 Bond angle restraints: 29907 Sorted by residual: angle pdb=" C ILE E 29 " pdb=" N LYS E 30 " pdb=" CA LYS E 30 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.50e+00 angle pdb=" C ILE L 29 " pdb=" N LYS L 30 " pdb=" CA LYS L 30 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.36e+00 angle pdb=" C ILE K 29 " pdb=" N LYS K 30 " pdb=" CA LYS K 30 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.34e+00 angle pdb=" C GLU I 87 " pdb=" N ASN I 88 " pdb=" CA ASN I 88 " ideal model delta sigma weight residual 121.54 126.66 -5.12 1.91e+00 2.74e-01 7.19e+00 angle pdb=" C GLU C 87 " pdb=" N ASN C 88 " pdb=" CA ASN C 88 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.08e+00 ... (remaining 29902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 13668 21.81 - 43.62: 1083 43.62 - 65.43: 177 65.43 - 87.25: 183 87.25 - 109.06: 87 Dihedral angle restraints: 15198 sinusoidal: 8085 harmonic: 7113 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.14 57.14 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.13 57.13 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.12 57.12 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 15195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3460 0.095 - 0.190: 311 0.190 - 0.284: 21 0.284 - 0.379: 3 0.379 - 0.474: 3 Chirality restraints: 3798 Sorted by residual: chirality pdb=" C1 BMA w 3 " pdb=" O4 NAG w 2 " pdb=" C2 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.61e+02 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.60e+02 chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-02 2.50e+03 5.59e+02 ... (remaining 3795 not shown) Planarity restraints: 3648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " 0.145 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" C7 NAG Z 1 " -0.041 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " -0.190 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.144 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG Z 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.108 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.188 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS G 216 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C HIS G 216 " -0.037 2.00e-02 2.50e+03 pdb=" O HIS G 216 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR G 217 " 0.012 2.00e-02 2.50e+03 ... (remaining 3645 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2178 2.74 - 3.28: 21339 3.28 - 3.82: 38018 3.82 - 4.36: 46857 4.36 - 4.90: 75626 Nonbonded interactions: 184018 Sorted by model distance: nonbonded pdb=" O ASN A 637 " pdb=" O HOH A 801 " model vdw 2.205 3.040 nonbonded pdb=" O SER G 460 " pdb=" OG1 THR G 461 " model vdw 2.212 3.040 nonbonded pdb=" O SER I 460 " pdb=" OG1 THR I 461 " model vdw 2.212 3.040 nonbonded pdb=" O SER C 460 " pdb=" OG1 THR C 461 " model vdw 2.212 3.040 nonbonded pdb=" O GLU B 634 " pdb=" O HOH B 801 " model vdw 2.218 3.040 ... (remaining 184013 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 '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '9' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain 'U' selection = chain 'l' } ncs_group { reference = chain '3' selection = chain 'AA' selection = chain 'O' selection = chain 'V' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'a' selection = chain 'h' selection = chain 'r' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 54.210 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.270 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:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22059 Z= 0.307 Angle : 0.750 6.455 29907 Z= 0.322 Chirality : 0.053 0.474 3798 Planarity : 0.004 0.119 3585 Dihedral : 19.291 109.057 10506 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.51 % Allowed : 18.41 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2448 helix: 2.17 (0.27), residues: 420 sheet: 0.46 (0.19), residues: 759 loop : 0.02 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 96 HIS 0.006 0.001 HIS I 216 PHE 0.014 0.001 PHE C 53 TYR 0.007 0.001 TYR L 91 ARG 0.003 0.000 ARG I 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 309 time to evaluate : 2.541 Fit side-chains REVERT: I 302 MET cc_start: 0.9279 (mmt) cc_final: 0.9027 (mmt) REVERT: L 69 THR cc_start: 0.8569 (m) cc_final: 0.8275 (m) outliers start: 11 outliers final: 7 residues processed: 316 average time/residue: 1.2169 time to fit residues: 442.5427 Evaluate side-chains 277 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 270 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain J residue 110 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 220 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 HIS G 130 GLN C 72 HIS C 94 ASN C 130 GLN I 72 HIS I 94 ASN I 130 GLN H 76 ASN L 38 GLN D 39 GLN E 34 ASN J 76 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22059 Z= 0.178 Angle : 0.590 7.978 29907 Z= 0.284 Chirality : 0.046 0.282 3798 Planarity : 0.003 0.042 3585 Dihedral : 12.903 77.792 5915 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.18 % Allowed : 17.29 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2448 helix: 2.52 (0.26), residues: 417 sheet: 0.65 (0.19), residues: 756 loop : 0.08 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 35 HIS 0.003 0.001 HIS E 49 PHE 0.011 0.001 PHE G 53 TYR 0.012 0.001 TYR L 91 ARG 0.007 0.000 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 279 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 621 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7691 (mt-10) REVERT: F 621 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7681 (mt-10) REVERT: H 72 ASP cc_start: 0.8802 (t70) cc_final: 0.8338 (t70) REVERT: D 72 ASP cc_start: 0.8786 (t70) cc_final: 0.8425 (t70) REVERT: D 77 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8603 (mmtm) REVERT: J 72 ASP cc_start: 0.8756 (t70) cc_final: 0.8415 (t70) outliers start: 47 outliers final: 27 residues processed: 310 average time/residue: 1.1921 time to fit residues: 427.7365 Evaluate side-chains 293 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN L 38 GLN E 38 GLN E 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 22059 Z= 0.368 Angle : 0.656 10.451 29907 Z= 0.315 Chirality : 0.049 0.307 3798 Planarity : 0.004 0.050 3585 Dihedral : 10.349 66.208 5907 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.83 % Allowed : 16.69 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2448 helix: 2.12 (0.26), residues: 423 sheet: 0.58 (0.18), residues: 771 loop : 0.07 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 35 HIS 0.003 0.001 HIS D 35 PHE 0.013 0.002 PHE G 353 TYR 0.016 0.002 TYR L 91 ARG 0.010 0.001 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 273 time to evaluate : 2.408 Fit side-chains revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7440 (tmt90) REVERT: B 621 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 621 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 155 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8118 (mttp) REVERT: C 500 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.8298 (mtt90) REVERT: F 585 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8045 (tmt90) REVERT: F 621 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7732 (mt-10) REVERT: I 155 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8166 (mttp) REVERT: I 302 MET cc_start: 0.9253 (mmt) cc_final: 0.8943 (mmt) REVERT: J 77 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8525 (ttmm) outliers start: 61 outliers final: 31 residues processed: 307 average time/residue: 1.2387 time to fit residues: 437.2615 Evaluate side-chains 293 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 258 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 585 ARG Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 234 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22059 Z= 0.198 Angle : 0.590 13.346 29907 Z= 0.282 Chirality : 0.047 0.348 3798 Planarity : 0.003 0.047 3585 Dihedral : 8.724 56.412 5907 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.69 % Allowed : 17.01 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2448 helix: 2.24 (0.26), residues: 423 sheet: 0.64 (0.18), residues: 780 loop : 0.14 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 35 HIS 0.002 0.001 HIS C 216 PHE 0.014 0.001 PHE J 67 TYR 0.014 0.001 TYR L 91 ARG 0.012 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 275 time to evaluate : 2.504 Fit side-chains REVERT: B 621 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7781 (mt-10) REVERT: G 500 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8286 (mtp-110) REVERT: A 621 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 117 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8488 (mtmt) REVERT: F 621 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7747 (mt-10) REVERT: I 302 MET cc_start: 0.9246 (mmt) cc_final: 0.8905 (mmt) REVERT: H 72 ASP cc_start: 0.8783 (t70) cc_final: 0.8549 (t70) REVERT: H 77 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8195 (ttmm) REVERT: D 72 ASP cc_start: 0.8764 (t70) cc_final: 0.8449 (t70) REVERT: D 77 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8313 (ttmm) REVERT: J 30 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9049 (pttt) REVERT: J 72 ASP cc_start: 0.8773 (t70) cc_final: 0.8530 (t70) REVERT: J 77 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8602 (ttmm) REVERT: K 33 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8398 (tm) outliers start: 58 outliers final: 29 residues processed: 312 average time/residue: 1.2800 time to fit residues: 460.7267 Evaluate side-chains 291 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 259 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 80 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 0.1980 chunk 174 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN E 24 GLN J 76 ASN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22059 Z= 0.304 Angle : 0.617 11.079 29907 Z= 0.296 Chirality : 0.047 0.308 3798 Planarity : 0.004 0.045 3585 Dihedral : 8.236 54.819 5907 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.74 % Allowed : 17.48 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2448 helix: 2.22 (0.26), residues: 420 sheet: 0.62 (0.18), residues: 774 loop : 0.13 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 35 HIS 0.002 0.001 HIS D 35 PHE 0.017 0.002 PHE J 67 TYR 0.010 0.001 TYR H 91 ARG 0.008 0.001 ARG D 82B *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 273 time to evaluate : 2.421 Fit side-chains revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 621 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 155 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8107 (mttp) REVERT: F 585 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8044 (tmt90) REVERT: F 621 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7773 (mt-10) REVERT: I 155 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8198 (mttp) REVERT: I 302 MET cc_start: 0.9277 (mmt) cc_final: 0.8943 (mmt) REVERT: H 77 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8369 (ttmm) REVERT: J 67 PHE cc_start: 0.8400 (m-10) cc_final: 0.8200 (m-80) REVERT: J 77 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8609 (ttmm) REVERT: K 33 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8412 (tm) outliers start: 59 outliers final: 37 residues processed: 311 average time/residue: 1.1983 time to fit residues: 430.8338 Evaluate side-chains 302 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 261 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 585 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 235 optimal weight: 0.4980 chunk 195 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN K 24 GLN K 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22059 Z= 0.181 Angle : 0.594 14.303 29907 Z= 0.282 Chirality : 0.046 0.330 3798 Planarity : 0.003 0.043 3585 Dihedral : 7.655 54.345 5907 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.13 % Allowed : 18.54 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2448 helix: 2.35 (0.26), residues: 420 sheet: 0.55 (0.19), residues: 747 loop : 0.15 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 35 HIS 0.004 0.001 HIS E 70 PHE 0.021 0.001 PHE H 67 TYR 0.008 0.001 TYR H 91 ARG 0.008 0.000 ARG D 82B *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 270 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 210 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: A 621 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7723 (mt-10) REVERT: C 103 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: F 621 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7748 (mt-10) REVERT: I 302 MET cc_start: 0.9247 (mmt) cc_final: 0.8927 (mmt) REVERT: H 72 ASP cc_start: 0.8756 (t70) cc_final: 0.8555 (t70) REVERT: H 77 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8338 (ttmm) REVERT: D 77 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8218 (ttmm) REVERT: J 77 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8580 (ttmm) REVERT: K 33 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8288 (tm) outliers start: 46 outliers final: 35 residues processed: 298 average time/residue: 1.2384 time to fit residues: 427.5052 Evaluate side-chains 296 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 258 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 146 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN E 24 GLN E 38 GLN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22059 Z= 0.290 Angle : 0.623 12.236 29907 Z= 0.297 Chirality : 0.047 0.298 3798 Planarity : 0.004 0.059 3585 Dihedral : 7.386 54.681 5907 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.78 % Allowed : 17.90 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2448 helix: 2.18 (0.26), residues: 423 sheet: 0.54 (0.19), residues: 744 loop : 0.10 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E 35 HIS 0.003 0.001 HIS J 35 PHE 0.039 0.002 PHE J 67 TYR 0.008 0.001 TYR H 91 ARG 0.012 0.001 ARG D 82B *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 270 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8623 (ttt180) REVERT: B 621 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7846 (mt-10) REVERT: G 210 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.6957 (m-10) REVERT: A 621 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 155 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8116 (mttp) REVERT: F 621 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7745 (mt-10) REVERT: I 155 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8167 (mttp) REVERT: I 302 MET cc_start: 0.9257 (mmt) cc_final: 0.8951 (mmt) REVERT: H 77 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8361 (ttmm) REVERT: D 77 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8324 (ttmm) REVERT: J 30 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9071 (pttt) REVERT: J 77 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8556 (ttmm) REVERT: K 33 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8322 (tm) outliers start: 60 outliers final: 37 residues processed: 308 average time/residue: 1.1961 time to fit residues: 424.7460 Evaluate side-chains 306 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 263 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.0060 chunk 45 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22059 Z= 0.172 Angle : 0.603 15.427 29907 Z= 0.285 Chirality : 0.045 0.305 3798 Planarity : 0.003 0.050 3585 Dihedral : 7.018 54.269 5907 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.99 % Allowed : 19.01 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2448 helix: 2.29 (0.26), residues: 423 sheet: 0.55 (0.19), residues: 747 loop : 0.16 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP K 35 HIS 0.004 0.001 HIS E 70 PHE 0.030 0.001 PHE J 67 TYR 0.015 0.001 TYR L 91 ARG 0.010 0.000 ARG D 82B *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 262 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7833 (mt-10) REVERT: G 207 LYS cc_start: 0.8684 (mppt) cc_final: 0.8452 (mmpt) REVERT: G 210 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6957 (m-10) REVERT: A 621 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7716 (mt-10) REVERT: F 621 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7768 (mt-10) REVERT: I 155 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8140 (mttp) REVERT: I 207 LYS cc_start: 0.8767 (mppt) cc_final: 0.8485 (mmpt) REVERT: I 210 PHE cc_start: 0.8130 (p90) cc_final: 0.6985 (m-10) REVERT: I 302 MET cc_start: 0.9250 (mmt) cc_final: 0.8933 (mmt) REVERT: H 77 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8350 (ttmm) REVERT: D 77 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8326 (ttmm) REVERT: J 30 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9048 (pttt) REVERT: J 77 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8525 (ttmm) REVERT: J 82 MET cc_start: 0.8153 (mpt) cc_final: 0.7903 (mpt) REVERT: J 83 ARG cc_start: 0.8069 (mpt-90) cc_final: 0.7810 (mmt90) REVERT: K 33 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8231 (tm) outliers start: 43 outliers final: 30 residues processed: 286 average time/residue: 1.1667 time to fit residues: 386.0111 Evaluate side-chains 290 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 197 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN E 38 GLN K 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22059 Z= 0.282 Angle : 0.632 12.904 29907 Z= 0.300 Chirality : 0.046 0.280 3798 Planarity : 0.004 0.066 3585 Dihedral : 6.948 54.758 5907 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.04 % Allowed : 19.38 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2448 helix: 1.95 (0.26), residues: 441 sheet: 0.59 (0.19), residues: 729 loop : 0.10 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 35 HIS 0.003 0.001 HIS I 72 PHE 0.029 0.002 PHE J 67 TYR 0.015 0.001 TYR L 91 ARG 0.014 0.001 ARG D 82B *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8636 (ttt180) REVERT: B 621 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 621 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 207 LYS cc_start: 0.8946 (mmpt) cc_final: 0.8708 (mppt) REVERT: F 585 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8058 (tmt90) REVERT: F 621 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7780 (mt-10) REVERT: I 155 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8166 (mttp) REVERT: I 207 LYS cc_start: 0.8770 (mppt) cc_final: 0.8496 (mmpt) REVERT: I 302 MET cc_start: 0.9293 (mmt) cc_final: 0.9017 (mmt) REVERT: H 77 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8387 (ttmm) REVERT: D 77 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8229 (ttmm) REVERT: J 30 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9094 (pttt) REVERT: J 77 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8324 (ttmm) REVERT: J 83 ARG cc_start: 0.8040 (mpt-90) cc_final: 0.7785 (mmt90) REVERT: K 33 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8244 (tm) outliers start: 44 outliers final: 33 residues processed: 291 average time/residue: 1.2557 time to fit residues: 420.5035 Evaluate side-chains 295 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 585 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.0970 chunk 140 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN K 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.210 22059 Z= 0.279 Angle : 0.890 59.190 29907 Z= 0.492 Chirality : 0.046 0.276 3798 Planarity : 0.004 0.056 3585 Dihedral : 6.945 54.783 5907 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.99 % Allowed : 19.80 % Favored : 78.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2448 helix: 1.97 (0.26), residues: 441 sheet: 0.59 (0.19), residues: 729 loop : 0.10 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 35 HIS 0.003 0.001 HIS I 72 PHE 0.025 0.002 PHE J 67 TYR 0.015 0.001 TYR L 91 ARG 0.006 0.000 ARG G 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 259 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 585 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8634 (ttt180) REVERT: B 621 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7819 (mt-10) REVERT: G 210 PHE cc_start: 0.7719 (p90) cc_final: 0.6974 (m-10) REVERT: A 621 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7666 (mt-10) REVERT: C 155 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8103 (mttp) REVERT: C 207 LYS cc_start: 0.8944 (mmpt) cc_final: 0.8706 (mppt) REVERT: F 585 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8043 (ttt180) REVERT: F 621 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7768 (mt-10) REVERT: I 155 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8164 (mttp) REVERT: I 302 MET cc_start: 0.9292 (mmt) cc_final: 0.8978 (mmt) REVERT: H 77 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8382 (ttmm) REVERT: D 77 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8221 (ttmm) REVERT: J 30 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9093 (pttt) REVERT: J 77 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8319 (ttmm) REVERT: J 82 MET cc_start: 0.7921 (mpp) cc_final: 0.7407 (mpt) REVERT: J 83 ARG cc_start: 0.8040 (mpt-90) cc_final: 0.7784 (mmt90) REVERT: K 33 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8238 (tm) outliers start: 43 outliers final: 31 residues processed: 287 average time/residue: 1.2684 time to fit residues: 418.4721 Evaluate side-chains 296 residues out of total 2157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 259 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 585 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 80 optimal weight: 0.0670 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058903 restraints weight = 40909.499| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.39 r_work: 0.2650 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.210 22059 Z= 0.279 Angle : 0.890 59.200 29907 Z= 0.492 Chirality : 0.046 0.276 3798 Planarity : 0.004 0.056 3585 Dihedral : 6.945 54.783 5907 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.72 % Allowed : 20.12 % Favored : 78.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2448 helix: 1.97 (0.26), residues: 441 sheet: 0.59 (0.19), residues: 729 loop : 0.10 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 35 HIS 0.003 0.001 HIS I 72 PHE 0.025 0.002 PHE J 67 TYR 0.015 0.001 TYR L 91 ARG 0.006 0.000 ARG G 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9271.49 seconds wall clock time: 163 minutes 32.63 seconds (9812.63 seconds total)