Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:41:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/12_2022/8dvd_27735_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/12_2022/8dvd_27735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/12_2022/8dvd_27735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/12_2022/8dvd_27735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/12_2022/8dvd_27735_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvd_27735/12_2022/8dvd_27735_updated_updated.pdb" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.056 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ASP 167": "OD1" <-> "OD2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 20804 Number of models: 1 Model: "" Number of chains: 83 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1059 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "C" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "E" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "F" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "G" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "P" 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: 3 Unresolved non-hydrogen chiralities: 5 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: 1 Unresolved non-hydrogen chiralities: 3 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: 1 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 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "Y" 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: 4 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "a" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "b" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "l" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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 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: 3 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 chiralities: 2 Chain: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "s" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "t" 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: 4 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "0" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "4" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "5" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "6" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "9" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "CA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "DA" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "EA" 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: 4 Unresolved non-hydrogen chiralities: 6 Chain: "FA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "GA" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "HA" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "IA" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "JA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "KA" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "LA" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "MA" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "NA" 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 chiralities: 2 Chain: "OA" 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 chiralities: 2 Chain: "PA" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "QA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "RA" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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 chiralities: 1 Time building chain proxies: 12.00, per 1000 atoms: 0.58 Number of scatterers: 20804 At special positions: 0 Unit cell: (147.288, 139.707, 162.45, 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 134 16.00 O 4755 8.00 N 3101 7.00 C 12814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 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 F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 149E" - pdb=" SG CYS E 149K" distance=2.02 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 149E" - pdb=" SG CYS F 149K" distance=2.03 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS G 149E" - pdb=" SG CYS G 149K" distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 191 " 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Y 4 " - " MAN Y 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN e 4 " - " MAN e 5 " " MAN f 4 " - " MAN f 5 " " MAN t 4 " - " MAN t 5 " " MAN x 4 " - " MAN x 5 " " MAN z 4 " - " MAN z 5 " " MANEA 4 " - " MANEA 5 " " MANIA 4 " - " MANIA 5 " " MANKA 4 " - " MANKA 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 4 3 " - " MAN 4 4 " " BMA 5 3 " - " MAN 5 4 " " BMA 7 3 " - " MAN 7 4 " " BMA 9 3 " - " MAN 9 4 " " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 6 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " " BMAEA 3 " - " MANEA 4 " " BMAGA 3 " - " MANGA 4 " " BMAIA 3 " - " MANIA 4 " " BMAJA 3 " - " MANJA 4 " " BMAKA 3 " - " MANKA 4 " " MANKA 6 " - " MANKA 7 " " BMALA 3 " - " MANLA 4 " " BMAPA 3 " - " MANPA 4 " " BMAQA 3 " - " MANQA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA 4 3 " - " MAN 4 5 " " BMA 9 3 " - " MAN 9 5 " " BMA M 3 " - " MAN M 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 6 " " BMA a 3 " - " MAN a 5 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA e 3 " - " MAN e 6 " " MAN e 6 " - " MAN e 8 " " BMA f 3 " - " MAN f 6 " " MAN f 6 " - " MAN f 8 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 5 " " BMA s 3 " - " MAN s 5 " " BMA t 3 " - " MAN t 6 " " BMA u 3 " - " MAN u 4 " " BMA v 3 " - " MAN v 5 " " BMA x 3 " - " MAN x 6 " " MAN x 6 " - " MAN x 7 " " BMA z 3 " - " MAN z 6 " " BMADA 3 " - " MANDA 5 " " BMAEA 3 " - " MANEA 6 " " BMAFA 3 " - " MANFA 4 " " BMAGA 3 " - " MANGA 5 " " BMAIA 3 " - " MANIA 6 " " MANIA 6 " - " MANIA 7 " " BMAKA 3 " - " MANKA 6 " " MANKA 6 " - " MANKA 8 " " BMALA 3 " - " MANLA 5 " " BMAPA 3 " - " MANPA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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 r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGLA 2 " - " BMALA 3 " " NAGMA 1 " - " NAGMA 2 " " NAGMA 2 " - " BMAMA 3 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGPA 2 " - " BMAPA 3 " " NAGQA 1 " - " NAGQA 2 " " NAGQA 2 " - " BMAQA 3 " " NAGRA 1 " - " NAGRA 2 " " NAGRA 2 " - " BMARA 3 " NAG-ASN " NAG 0 1 " - " ASN F 160 " " NAG 1 1 " - " ASN F 173 " " NAG 2 1 " - " ASN F 185B" " NAG 3 1 " - " ASN F 354E" " NAG 4 1 " - " ASN F 280 " " NAG 5 1 " - " ASN F 301 " " NAG 6 1 " - " ASN F 468 " " NAG 7 1 " - " ASN G 97 " " NAG 8 1 " - " ASN G 88 " " NAG 9 1 " - " ASN G 132 " " NAG D 1 " - " ASN A 612 " " NAG E 601 " - " ASN E 464 " " NAG F 602 " - " ASN F 464 " " NAG G 601 " - " ASN G 464 " " NAG I 1 " - " ASN A 625 " " NAG J 1 " - " ASN A 641 " " NAG K 1 " - " ASN B 612 " " NAG M 1 " - " ASN B 625 " " NAG N 1 " - " ASN B 641 " " NAG O 1 " - " ASN C 612 " " NAG P 1 " - " ASN C 625 " " NAG Q 1 " - " ASN C 641 " " NAG R 1 " - " ASN E 97 " " NAG S 1 " - " ASN E 88 " " NAG T 1 " - " ASN E 132 " " NAG U 1 " - " ASN E 187 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 229 " " NAG X 1 " - " ASN E 446 " " NAG Y 1 " - " ASN E 360 " " NAG Z 1 " - " ASN E 267A" " NAG a 1 " - " ASN E 291 " " NAG b 1 " - " ASN E 149 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 149J" " NAG e 1 " - " ASN E 47 " " NAG f 1 " - " ASN E 160 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 185B" " NAG i 1 " - " ASN E 354E" " NAG j 1 " - " ASN E 280 " " NAG k 1 " - " ASN E 468 " " NAG l 1 " - " ASN E 173 " " NAG m 1 " - " ASN F 97 " " NAG n 1 " - " ASN F 88 " " NAG o 1 " - " ASN F 132 " " NAG p 1 " - " ASN F 187 " " NAG q 1 " - " ASN F 197 " " NAG r 1 " - " ASN F 229 " " NAG s 1 " - " ASN F 446 " " NAG t 1 " - " ASN F 360 " " NAG u 1 " - " ASN F 267A" " NAG v 1 " - " ASN F 291 " " NAG w 1 " - " ASN F 149 " " NAG x 1 " - " ASN F 262 " " NAG y 1 " - " ASN F 149J" " NAG z 1 " - " ASN F 47 " " NAGAA 1 " - " ASN G 187 " " NAGBA 1 " - " ASN G 197 " " NAGCA 1 " - " ASN G 229 " " NAGDA 1 " - " ASN G 446 " " NAGEA 1 " - " ASN G 360 " " NAGFA 1 " - " ASN G 267A" " NAGGA 1 " - " ASN G 291 " " NAGHA 1 " - " ASN G 149 " " NAGIA 1 " - " ASN G 262 " " NAGJA 1 " - " ASN G 149J" " NAGKA 1 " - " ASN G 47 " " NAGLA 1 " - " ASN G 160 " " NAGMA 1 " - " ASN G 173 " " NAGNA 1 " - " ASN G 185B" " NAGOA 1 " - " ASN G 354E" " NAGPA 1 " - " ASN G 280 " " NAGQA 1 " - " ASN G 468 " " NAGRA 1 " - " ASN G 301 " Time building additional restraints: 13.54 Conformation dependent library (CDL) restraints added in 2.7 seconds 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 31 sheets defined 22.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 513 through 527 removed outlier: 3.943A pdb=" N PHE A 522 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 removed outlier: 3.570A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 595 removed outlier: 3.569A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 663 removed outlier: 4.561A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASN A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 525 removed outlier: 4.445A pdb=" N PHE B 522 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU B 523 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 552 removed outlier: 3.966A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 596 removed outlier: 3.535A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 589 " --> pdb=" O LYS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 663 removed outlier: 4.493A pdb=" N PHE B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 522 through 525 removed outlier: 3.744A pdb=" N THR C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 525' Processing helix chain 'C' and resid 539 through 552 removed outlier: 3.728A pdb=" N ALA C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 596 Processing helix chain 'C' and resid 628 through 663 removed outlier: 3.510A pdb=" N ARG C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS C 634 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.015A pdb=" N ARG E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 149E through 149H No H-bonds generated for 'chain 'E' and resid 149E through 149H' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.958A pdb=" N GLU E 344 " --> pdb=" O ASP E 340 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 395 removed outlier: 3.638A pdb=" N GLU E 395 " --> pdb=" O LEU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 409 No H-bonds generated for 'chain 'E' and resid 407 through 409' Processing helix chain 'E' and resid 475 through 482 removed outlier: 3.579A pdb=" N GLU E 482 " --> pdb=" O TYR E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.592A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 133 through 139 removed outlier: 3.764A pdb=" N TRP F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 288 through 290 No H-bonds generated for 'chain 'F' and resid 288 through 290' Processing helix chain 'F' and resid 339 through 351 removed outlier: 3.536A pdb=" N LYS F 343 " --> pdb=" O LYS F 339 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 372 No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 388 through 395 Processing helix chain 'F' and resid 407 through 409 No H-bonds generated for 'chain 'F' and resid 407 through 409' Processing helix chain 'F' and resid 476 through 483 removed outlier: 3.777A pdb=" N LEU F 483 " --> pdb=" O ARG F 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.616A pdb=" N TRP G 109 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 125 removed outlier: 3.600A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 125' Processing helix chain 'G' and resid 133 through 138 removed outlier: 3.749A pdb=" N ARG G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 149E through 149H No H-bonds generated for 'chain 'G' and resid 149E through 149H' Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 339 through 351 removed outlier: 3.572A pdb=" N GLU G 344 " --> pdb=" O ASP G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 372 No H-bonds generated for 'chain 'G' and resid 369 through 372' Processing helix chain 'G' and resid 388 through 394 Processing helix chain 'G' and resid 475 through 482 removed outlier: 3.719A pdb=" N LEU G 478 " --> pdb=" O VAL G 475 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR G 479 " --> pdb=" O ALA G 476 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU G 482 " --> pdb=" O TYR G 479 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 30 removed outlier: 3.549A pdb=" N SER H 28 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.052A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 215 through 218 Processing sheet with id= D, first strand: chain 'E' and resid 157 through 159 removed outlier: 3.696A pdb=" N GLU E 174 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE E 159 " --> pdb=" O TYR E 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.548A pdb=" N VAL E 182 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= G, first strand: chain 'E' and resid 293 through 298 removed outlier: 4.201A pdb=" N LEU E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 305 through 308 removed outlier: 3.593A pdb=" N SER E 317 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 360 through 362 removed outlier: 3.581A pdb=" N THR E 362 " --> pdb=" O ILE E 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET E 471 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.717A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.876A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 215 through 218 Processing sheet with id= M, first strand: chain 'F' and resid 271 through 273 removed outlier: 7.084A pdb=" N ASN F 360 " --> pdb=" O ILE F 469 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET F 471 " --> pdb=" O ASN F 360 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR F 362 " --> pdb=" O MET F 471 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 293 through 298 removed outlier: 4.093A pdb=" N LEU F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.864A pdb=" N CYS F 378 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 423 through 425 removed outlier: 3.529A pdb=" N ILE F 424 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 35 through 40 Processing sheet with id= R, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.759A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= T, first strand: chain 'G' and resid 129 through 132 Processing sheet with id= U, first strand: chain 'G' and resid 155 through 159 removed outlier: 3.658A pdb=" N CYS G 157 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 271 through 274 removed outlier: 4.479A pdb=" N ARG G 281 " --> pdb=" O HIS G 274 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA G 454 " --> pdb=" O THR G 282 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 293 through 298 removed outlier: 3.636A pdb=" N ARG G 298 " --> pdb=" O LEU G 443 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 360 through 362 Processing sheet with id= Y, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.584A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 423 through 425 Processing sheet with id= AA, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= AB, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.741A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP H 50 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY H 56 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 100 through 100E removed outlier: 6.767A pdb=" N GLU H 100O" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE H 100D" --> pdb=" O TYR H 100M" (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR H 100M" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.528A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.845A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU L 105 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1179 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: 5.93 Time building geometry restraints manager: 14.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2963 1.31 - 1.44: 6629 1.44 - 1.57: 11427 1.57 - 1.70: 3 1.70 - 1.83: 181 Bond restraints: 21203 Sorted by residual: bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.576 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.599 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CZ TYS H 100I" pdb=" OH TYS H 100I" ideal model delta sigma weight residual 1.371 1.433 -0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" CZ TYS H 100F" pdb=" OH TYS H 100F" ideal model delta sigma weight residual 1.371 1.428 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C LEU B 663 " pdb=" N ASN B 664 " ideal model delta sigma weight residual 1.329 1.292 0.037 1.40e-02 5.10e+03 6.94e+00 ... (remaining 21198 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.17: 455 106.17 - 113.15: 13594 113.15 - 120.14: 6390 120.14 - 127.13: 8115 127.13 - 134.12: 274 Bond angle restraints: 28828 Sorted by residual: angle pdb=" CA LEU C 663 " pdb=" C LEU C 663 " pdb=" N ASN C 664 " ideal model delta sigma weight residual 117.07 110.48 6.59 1.14e+00 7.69e-01 3.34e+01 angle pdb=" CA CYS G 205 " pdb=" CB CYS G 205 " pdb=" SG CYS G 205 " ideal model delta sigma weight residual 114.40 124.92 -10.52 2.30e+00 1.89e-01 2.09e+01 angle pdb=" CA LEU C 663 " pdb=" C LEU C 663 " pdb=" O LEU C 663 " ideal model delta sigma weight residual 120.82 125.16 -4.34 1.05e+00 9.07e-01 1.71e+01 angle pdb=" CA LEU A 663 " pdb=" C LEU A 663 " pdb=" N ASN A 664 " ideal model delta sigma weight residual 117.07 112.70 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" C2 NAG K 2 " pdb=" N2 NAG K 2 " pdb=" C7 NAG K 2 " ideal model delta sigma weight residual 123.12 127.46 -4.34 1.28e+00 6.08e-01 1.14e+01 ... (remaining 28823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 11759 19.27 - 38.54: 919 38.54 - 57.81: 152 57.81 - 77.09: 29 77.09 - 96.36: 16 Dihedral angle restraints: 12875 sinusoidal: 6660 harmonic: 6215 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 -162.71 76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual 93.00 153.06 -60.06 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CA CYS G 119 " pdb=" C CYS G 119 " pdb=" N VAL G 120 " pdb=" CA VAL G 120 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 12872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 4104 0.286 - 0.572: 8 0.572 - 0.858: 4 0.858 - 1.144: 1 1.144 - 1.429: 1 Chirality restraints: 4118 Sorted by residual: 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 -2.56 0.16 2.00e-02 2.50e+03 6.77e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN E 160 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.99e+01 ... (remaining 4115 not shown) Planarity restraints: 3247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 160 " -0.032 2.00e-02 2.50e+03 3.69e-02 1.70e+01 pdb=" CG ASN E 160 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 160 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN E 160 " 0.062 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 120 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C VAL G 120 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL G 120 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS G 121 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 318 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO E 319 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 319 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 319 " -0.036 5.00e-02 4.00e+02 ... (remaining 3244 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 213 2.53 - 3.12: 17396 3.12 - 3.71: 28813 3.71 - 4.31: 41824 4.31 - 4.90: 65893 Nonbonded interactions: 154139 Sorted by model distance: nonbonded pdb=" O3 NAGKA 1 " pdb=" O5 NAGKA 2 " model vdw 1.932 2.440 nonbonded pdb=" O3 NAGNA 1 " pdb=" O5 NAGNA 2 " model vdw 2.052 2.440 nonbonded pdb=" O3 NAG e 1 " pdb=" O5 NAG e 2 " model vdw 2.059 2.440 nonbonded pdb=" O3 NAG 2 1 " pdb=" O5 NAG 2 2 " model vdw 2.061 2.440 nonbonded pdb=" O3 NAG T 2 " pdb=" O5 BMA T 3 " model vdw 2.099 2.440 ... (remaining 154134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain '9' selection = chain 'DA' selection = chain 'GA' selection = chain 'LA' selection = chain 'M' selection = chain 'P' selection = chain 'PA' selection = chain 'T' selection = chain 'X' selection = chain 'a' selection = chain 'j' selection = chain 'o' selection = chain 's' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '6' selection = chain 'HA' selection = chain 'J' selection = chain 'MA' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'RA' selection = chain 'U' selection = chain 'Z' selection = chain 'b' selection = chain 'k' selection = chain 'l' selection = chain 'w' } ncs_group { reference = chain '2' selection = chain '3' selection = chain '8' selection = chain 'AA' selection = chain 'NA' selection = chain 'OA' selection = chain 'S' selection = chain 'h' selection = chain 'i' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'BA' selection = chain 'CA' selection = chain 'D' selection = chain 'FA' selection = chain 'I' selection = chain 'JA' selection = chain 'K' selection = chain 'O' selection = chain 'QA' selection = chain 'V' selection = chain 'W' selection = chain 'd' selection = chain 'g' selection = chain 'm' selection = chain 'q' selection = chain 'r' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 512 through 557 or resid 572 through 664)) selection = (chain 'C' and (resid 512 through 557 or resid 572 through 664)) } ncs_group { reference = (chain 'E' and resid 33 through 505) selection = (chain 'F' and resid 33 through 505) selection = (chain 'G' and resid 33 through 505) } ncs_group { reference = (chain 'EA' and (resid 1 or resid 4 through 6)) selection = (chain 'IA' and (resid 2 or resid 5 through 7)) selection = (chain 'Y' and (resid 1 or resid 4 through 6)) selection = (chain 't' and (resid 1 or resid 4 through 6)) selection = (chain 'x' and (resid 2 or resid 5 through 7)) selection = (chain 'z' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'KA' selection = chain 'c' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 12814 2.51 5 N 3101 2.21 5 O 4755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 9.060 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.190 Process input model: 56.000 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.004 0.103 21203 Z= 0.225 Angle : 0.558 10.524 28828 Z= 0.305 Chirality : 0.052 1.429 4118 Planarity : 0.003 0.065 3172 Dihedral : 13.052 96.357 8742 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.97 % Favored : 91.94 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 2109 helix: 1.71 (0.28), residues: 354 sheet: -0.33 (0.23), residues: 551 loop : -1.31 (0.18), residues: 1204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 350 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 363 average time/residue: 0.3535 time to fit residues: 190.4701 Evaluate side-chains 162 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 2.152 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1773 time to fit residues: 4.3910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 629 GLN B 540 GLN ** B 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN E 103 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS L 42 GLN L 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 21203 Z= 0.340 Angle : 0.711 9.725 28828 Z= 0.389 Chirality : 0.049 0.892 4118 Planarity : 0.005 0.049 3172 Dihedral : 7.321 92.315 4739 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.27 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2109 helix: 1.28 (0.26), residues: 365 sheet: -0.74 (0.24), residues: 500 loop : -1.35 (0.18), residues: 1244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 205 average time/residue: 0.3386 time to fit residues: 108.1342 Evaluate side-chains 138 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 2.163 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1943 time to fit residues: 4.2447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 540 GLN C 602 GLN ** E 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 323 ASN F 347 GLN G 254 GLN L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 21203 Z= 0.258 Angle : 0.655 8.622 28828 Z= 0.359 Chirality : 0.047 0.824 4118 Planarity : 0.004 0.049 3172 Dihedral : 7.305 88.573 4739 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.54 % Favored : 92.37 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2109 helix: 1.00 (0.26), residues: 386 sheet: -0.62 (0.23), residues: 535 loop : -1.38 (0.18), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 197 average time/residue: 0.3222 time to fit residues: 98.7871 Evaluate side-chains 130 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 2.177 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1777 time to fit residues: 3.4434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 182 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 HIS E 428 HIS F 323 ASN G 254 GLN L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 21203 Z= 0.227 Angle : 0.635 13.029 28828 Z= 0.344 Chirality : 0.047 0.771 4118 Planarity : 0.004 0.049 3172 Dihedral : 7.202 86.748 4739 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.40 % Favored : 92.46 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2109 helix: 0.95 (0.26), residues: 384 sheet: -0.51 (0.23), residues: 514 loop : -1.45 (0.18), residues: 1211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 193 average time/residue: 0.3508 time to fit residues: 105.0338 Evaluate side-chains 128 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 2.188 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1839 time to fit residues: 3.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 0.0970 chunk 174 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 410 GLN G 254 GLN L 27 HIS L 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 21203 Z= 0.233 Angle : 0.635 13.808 28828 Z= 0.342 Chirality : 0.047 0.777 4118 Planarity : 0.004 0.048 3172 Dihedral : 7.173 85.532 4739 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.78 % Favored : 92.08 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2109 helix: 0.93 (0.27), residues: 386 sheet: -0.56 (0.23), residues: 516 loop : -1.42 (0.18), residues: 1207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.3199 time to fit residues: 85.3398 Evaluate side-chains 119 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 629 GLN C 540 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN F 202 GLN G 254 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 21203 Z= 0.287 Angle : 0.659 13.641 28828 Z= 0.356 Chirality : 0.047 0.748 4118 Planarity : 0.004 0.051 3172 Dihedral : 7.273 86.985 4739 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.39 % Favored : 91.51 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2109 helix: 0.81 (0.27), residues: 385 sheet: -0.52 (0.25), residues: 433 loop : -1.37 (0.17), residues: 1291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.3015 time to fit residues: 75.7760 Evaluate side-chains 114 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2170 time to fit residues: 3.2777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN C 575 ASN C 629 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN G 254 GLN G 410 GLN G 411 HIS G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27CGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 21203 Z= 0.380 Angle : 0.740 14.673 28828 Z= 0.399 Chirality : 0.050 0.784 4118 Planarity : 0.005 0.068 3172 Dihedral : 7.634 88.434 4739 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.06 % Favored : 90.85 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2109 helix: 0.61 (0.27), residues: 379 sheet: -0.55 (0.24), residues: 462 loop : -1.52 (0.17), residues: 1268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.3036 time to fit residues: 74.9074 Evaluate side-chains 115 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.415 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2488 time to fit residues: 3.6487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 121 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.0010 chunk 159 optimal weight: 0.0040 chunk 184 optimal weight: 0.8980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 653 GLN C 575 ASN C 629 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN G 254 GLN G 428 HIS ** L 27CGLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 21203 Z= 0.219 Angle : 0.657 11.730 28828 Z= 0.354 Chirality : 0.047 0.741 4118 Planarity : 0.004 0.065 3172 Dihedral : 7.337 88.501 4739 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.49 % Favored : 92.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2109 helix: 1.00 (0.27), residues: 366 sheet: -0.25 (0.26), residues: 397 loop : -1.39 (0.17), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3092 time to fit residues: 81.9993 Evaluate side-chains 122 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8665 > 50: distance: 0 - 10: 3.022 distance: 118 - 192: 21.850 distance: 121 - 189: 15.143 distance: 138 - 142: 17.122 distance: 142 - 143: 11.429 distance: 143 - 144: 14.410 distance: 143 - 146: 14.141 distance: 144 - 145: 17.611 distance: 144 - 152: 25.522 distance: 146 - 147: 17.803 distance: 147 - 148: 7.354 distance: 147 - 149: 24.473 distance: 148 - 150: 7.044 distance: 150 - 151: 25.797 distance: 152 - 153: 24.061 distance: 153 - 154: 6.686 distance: 153 - 156: 22.855 distance: 154 - 155: 19.138 distance: 154 - 161: 10.701 distance: 156 - 157: 4.822 distance: 157 - 158: 27.106 distance: 158 - 159: 30.033 distance: 159 - 160: 7.106 distance: 161 - 162: 8.807 distance: 162 - 163: 7.511 distance: 162 - 165: 5.508 distance: 163 - 164: 6.752 distance: 163 - 168: 12.560 distance: 165 - 166: 8.507 distance: 165 - 167: 10.170 distance: 168 - 169: 12.024 distance: 169 - 170: 5.845 distance: 170 - 172: 13.820 distance: 172 - 173: 3.612 distance: 173 - 174: 5.258 distance: 173 - 176: 7.203 distance: 174 - 175: 28.891 distance: 174 - 181: 33.263 distance: 176 - 177: 8.844 distance: 177 - 178: 6.787 distance: 178 - 179: 8.989 distance: 179 - 180: 14.138 distance: 181 - 182: 5.871 distance: 182 - 183: 19.538 distance: 182 - 185: 4.684 distance: 183 - 184: 7.263 distance: 183 - 189: 10.387 distance: 185 - 186: 3.801 distance: 186 - 187: 11.911 distance: 186 - 188: 8.450 distance: 189 - 190: 6.105 distance: 190 - 191: 9.920 distance: 190 - 193: 12.306 distance: 191 - 192: 7.072 distance: 191 - 196: 17.906 distance: 193 - 194: 10.702 distance: 193 - 195: 29.467 distance: 196 - 197: 4.446 distance: 197 - 198: 13.164 distance: 197 - 200: 6.186 distance: 198 - 199: 15.885 distance: 198 - 208: 22.295 distance: 200 - 201: 13.168 distance: 201 - 202: 12.306 distance: 201 - 203: 10.192 distance: 202 - 204: 10.284 distance: 203 - 205: 14.620 distance: 204 - 206: 6.356 distance: 205 - 206: 14.058 distance: 206 - 207: 11.938 distance: 208 - 209: 15.819 distance: 209 - 210: 12.942 distance: 209 - 212: 13.700 distance: 210 - 211: 16.049 distance: 210 - 216: 17.323 distance: 212 - 213: 10.876 distance: 213 - 214: 21.227 distance: 213 - 215: 23.674 distance: 216 - 217: 30.076 distance: 216 - 222: 20.959 distance: 217 - 218: 15.700 distance: 217 - 220: 23.287 distance: 218 - 219: 14.231 distance: 218 - 223: 29.218 distance: 220 - 221: 23.751 distance: 221 - 222: 21.299