Starting phenix.real_space_refine on Sun Aug 11 00:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/08_2024/5szs_8331.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/08_2024/5szs_8331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/08_2024/5szs_8331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/08_2024/5szs_8331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/08_2024/5szs_8331.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5szs_8331/08_2024/5szs_8331.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19089 2.51 5 N 4743 2.21 5 O 6345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 922": "OD1" <-> "OD2" Residue "A PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1137": "OD1" <-> "OD2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 922": "OD1" <-> "OD2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1137": "OD1" <-> "OD2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 922": "OD1" <-> "OD2" Residue "C PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1137": "OD1" <-> "OD2" Residue "C TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.87s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30306 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "C" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9141 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 41, 'TRANS': 1135} Chain breaks: 3 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "BA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 16.96, per 1000 atoms: 0.56 Number of scatterers: 30306 At special positions: 0 Unit cell: (150.96, 141.44, 178.16, 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 129 16.00 O 6345 8.00 N 4743 7.00 C 19089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 181 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 210 " distance=2.21 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 351 " distance=2.04 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 497 " - pdb=" SG CYS A 500 " distance=2.04 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 567 " distance=2.05 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 577 " distance=2.02 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 678 " distance=2.25 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 737 " distance=2.02 Simple disulfide: pdb=" SG CYS A 789 " - pdb=" SG CYS A 811 " distance=2.07 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS A 800 " distance=2.02 Simple disulfide: pdb=" SG CYS A 896 " - pdb=" SG CYS A 907 " distance=2.04 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1109 " distance=2.02 Simple disulfide: pdb=" SG CYS A1148 " - pdb=" SG CYS A1195 " distance=1.74 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 181 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 210 " distance=2.21 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 438 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 500 " distance=2.04 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 567 " distance=2.05 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 577 " distance=2.02 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 678 " distance=2.25 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 737 " distance=2.02 Simple disulfide: pdb=" SG CYS B 789 " - pdb=" SG CYS B 811 " distance=2.07 Simple disulfide: pdb=" SG CYS B 794 " - pdb=" SG CYS B 800 " distance=2.02 Simple disulfide: pdb=" SG CYS B 896 " - pdb=" SG CYS B 907 " distance=2.04 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1109 " distance=2.02 Simple disulfide: pdb=" SG CYS B1148 " - pdb=" SG CYS B1195 " distance=1.74 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 181 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 210 " distance=2.21 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 351 " distance=2.04 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 497 " - pdb=" SG CYS C 500 " distance=2.04 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 567 " distance=2.05 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 678 " distance=2.25 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 737 " distance=2.02 Simple disulfide: pdb=" SG CYS C 789 " - pdb=" SG CYS C 811 " distance=2.07 Simple disulfide: pdb=" SG CYS C 794 " - pdb=" SG CYS C 800 " distance=2.02 Simple disulfide: pdb=" SG CYS C 896 " - pdb=" SG CYS C 907 " distance=2.04 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1109 " distance=2.02 Simple disulfide: pdb=" SG CYS C1148 " - pdb=" SG CYS C1195 " distance=1.74 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 Atom "HETATM28675 O4 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM27812 O4 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM29538 O4 NAG 1 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 0 4 " - " MAN 0 5 " " MAN 0 5 " - " MAN 0 6 " " MAN D 4 " - " MAN D 5 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN Y 4 " - " MAN Y 5 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " MAN 0 7 " - " MAN 0 8 " " BMA 3 3 " - " MAN 3 4 " " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 8 " " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA i 3 " - " MAN i 4 " " BMA p 3 " - " MAN p 4 " " BMA q 3 " - " MAN q 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 7 " " BMA 3 3 " - " MAN 3 5 " " BMA D 3 " - " MAN D 6 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 7 " " BMA N 3 " - " MAN N 5 " " BMA V 3 " - " MAN V 5 " " BMA Y 3 " - " MAN Y 6 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 7 " " BMA i 3 " - " MAN i 5 " " BMA q 3 " - " MAN q 5 " " BMA t 3 " - " MAN t 6 " " BMA x 3 " - " MAN x 4 " " BMABA 3 " - " MANBA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN C 426 " " NAG 1 1 " - " ASN C 486 " " NAG 2 1 " - " ASN C 506 " " NAG 3 1 " - " ASN C 666 " " NAG 4 1 " - " ASN C 699 " " NAG 5 1 " - " ASN C 723 " " NAG 6 1 " - " ASN C 749 " " NAG 7 1 " - " ASN C 762 " " NAG 8 1 " - " ASN C 768 " " NAG 9 1 " - " ASN C 844 " " NAG A1401 " - " ASN A 155 " " NAG A1402 " - " ASN A 187 " " NAG A1403 " - " ASN A 193 " " NAG A1439 " - " ASN A 512 " " NAG A1440 " - " ASN A 626 " " NAG A1441 " - " ASN A 645 " " NAG A1474 " - " ASN A1218 " " NAG B1401 " - " ASN B 155 " " NAG B1402 " - " ASN B 187 " " NAG B1403 " - " ASN B 193 " " NAG B1439 " - " ASN B 512 " " NAG B1440 " - " ASN B 626 " " NAG B1441 " - " ASN B 645 " " NAG B1474 " - " ASN B1218 " " NAG C1401 " - " ASN C 155 " " NAG C1402 " - " ASN C 187 " " NAG C1403 " - " ASN C 193 " " NAG C1439 " - " ASN C 512 " " NAG C1440 " - " ASN C 626 " " NAG C1441 " - " ASN C 645 " " NAG C1474 " - " ASN C1218 " " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN A 301 " " NAG G 1 " - " ASN A 330 " " NAG H 1 " - " ASN A 354 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 403 " " NAG K 1 " - " ASN A 426 " " NAG L 1 " - " ASN A 486 " " NAG M 1 " - " ASN A 506 " " NAG N 1 " - " ASN A 666 " " NAG O 1 " - " ASN A 699 " " NAG P 1 " - " ASN A 723 " " NAG Q 1 " - " ASN A 749 " " NAG R 1 " - " ASN A 762 " " NAG S 1 " - " ASN A 768 " " NAG T 1 " - " ASN A 844 " " NAG U 1 " - " ASN A 852 " " NAG V 1 " - " ASN A1111 " " NAG W 1 " - " ASN A1196 " " NAG X 1 " - " ASN A1201 " " NAG Y 1 " - " ASN B 240 " " NAG Z 1 " - " ASN B 276 " " NAG a 1 " - " ASN B 301 " " NAG b 1 " - " ASN B 330 " " NAG c 1 " - " ASN B 354 " " NAG d 1 " - " ASN B 358 " " NAG e 1 " - " ASN B 403 " " NAG f 1 " - " ASN B 426 " " NAG g 1 " - " ASN B 486 " " NAG h 1 " - " ASN B 506 " " NAG i 1 " - " ASN B 666 " " NAG j 1 " - " ASN B 699 " " NAG k 1 " - " ASN B 723 " " NAG l 1 " - " ASN B 749 " " NAG m 1 " - " ASN B 762 " " NAG n 1 " - " ASN B 768 " " NAG o 1 " - " ASN B 844 " " NAG p 1 " - " ASN B 852 " " NAG q 1 " - " ASN B1111 " " NAG r 1 " - " ASN B1196 " " NAG s 1 " - " ASN B1201 " " NAG t 1 " - " ASN C 240 " " NAG u 1 " - " ASN C 276 " " NAG v 1 " - " ASN C 301 " " NAG w 1 " - " ASN C 330 " " NAG x 1 " - " ASN C 354 " " NAG y 1 " - " ASN C 358 " " NAG z 1 " - " ASN C 403 " " NAGAA 1 " - " ASN C 852 " " NAGBA 1 " - " ASN C1111 " " NAGCA 1 " - " ASN C1196 " " NAGDA 1 " - " ASN C1201 " Time building additional restraints: 15.41 Conformation dependent library (CDL) restraints added in 4.6 seconds 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 25.1% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY A 849 " --> pdb=" O THR A 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 850 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR A 897 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 922 through 936 Processing helix chain 'A' and resid 949 through 960 Processing helix chain 'A' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1031 Processing helix chain 'A' and resid 1032 through 1034 No H-bonds generated for 'chain 'A' and resid 1032 through 1034' Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1216 through 1224 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.572A pdb=" N ARG B 225 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 536 through 539 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 799 through 804 Processing helix chain 'B' and resid 807 through 833 removed outlier: 4.801A pdb=" N THR B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 832 " --> pdb=" O ASP B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 844 through 852 removed outlier: 4.138A pdb=" N GLY B 849 " --> pdb=" O THR B 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 850 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 882 Processing helix chain 'B' and resid 892 through 898 removed outlier: 4.118A pdb=" N THR B 897 " --> pdb=" O LYS B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 922 through 936 Processing helix chain 'B' and resid 949 through 960 Processing helix chain 'B' and resid 969 through 992 removed outlier: 4.482A pdb=" N LYS B 973 " --> pdb=" O GLN B 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1031 Processing helix chain 'B' and resid 1032 through 1034 No H-bonds generated for 'chain 'B' and resid 1032 through 1034' Processing helix chain 'B' and resid 1042 through 1048 Processing helix chain 'B' and resid 1051 through 1099 removed outlier: 5.115A pdb=" N GLN B1057 " --> pdb=" O ILE B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1205 through 1210 Processing helix chain 'B' and resid 1216 through 1224 Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.640A pdb=" N ASN C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.571A pdb=" N ARG C 225 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 530 through 534 Processing helix chain 'C' and resid 536 through 539 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 799 through 804 Processing helix chain 'C' and resid 807 through 833 removed outlier: 4.802A pdb=" N THR C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 832 " --> pdb=" O ASP C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 844 through 852 removed outlier: 4.137A pdb=" N GLY C 849 " --> pdb=" O THR C 846 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP C 850 " --> pdb=" O SER C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 882 Processing helix chain 'C' and resid 892 through 898 removed outlier: 4.117A pdb=" N THR C 897 " --> pdb=" O LYS C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 911 Processing helix chain 'C' and resid 922 through 936 Processing helix chain 'C' and resid 949 through 960 Processing helix chain 'C' and resid 969 through 992 removed outlier: 4.481A pdb=" N LYS C 973 " --> pdb=" O GLN C 969 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1031 Processing helix chain 'C' and resid 1032 through 1034 No H-bonds generated for 'chain 'C' and resid 1032 through 1034' Processing helix chain 'C' and resid 1042 through 1048 Processing helix chain 'C' and resid 1051 through 1099 removed outlier: 5.114A pdb=" N GLN C1057 " --> pdb=" O ILE C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1185 through 1187 No H-bonds generated for 'chain 'C' and resid 1185 through 1187' Processing helix chain 'C' and resid 1205 through 1210 Processing helix chain 'C' and resid 1216 through 1224 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR A 191 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 206 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 204 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 195 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA A 99 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 133 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 101 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A 131 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 103 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 129 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 105 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 125 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 161 removed outlier: 3.720A pdb=" N GLY A 62 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A 299 " --> pdb=" O TRP A 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 415 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG A 297 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE A 417 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 295 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 384 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL A 248 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 427 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG A 250 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 425 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A 252 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 423 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 421 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 417 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 260 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 415 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP A 413 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP A 422 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR A 437 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 424 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 435 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A 426 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 328 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 313 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR A 356 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP A 323 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE A 326 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN A 683 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A 694 " --> pdb=" O GLN A 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 685 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU A 662 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR A 654 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 504 through 509 removed outlier: 6.457A pdb=" N SER A 601 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 603 " --> pdb=" O LYS A 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A 562 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP A 585 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 581 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 595 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 579 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR A 597 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS A 577 " --> pdb=" O TYR A 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE A 736 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR A 730 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A1133 " --> pdb=" O HIS A1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A1114 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN A 762 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A1142 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 764 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A1140 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1138 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 768 " --> pdb=" O THR A1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS A1142 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A1164 " --> pdb=" O TRP A1144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE A1202 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR B 191 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 206 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 204 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR B 195 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA B 99 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 133 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 101 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B 131 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 103 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B 129 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 105 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 125 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY B 62 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN B 299 " --> pdb=" O TRP B 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 415 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 297 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE B 417 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 295 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 384 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 247 through 262 removed outlier: 5.506A pdb=" N VAL B 248 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 427 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG B 250 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 425 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 252 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 423 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 421 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 417 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 260 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 415 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP B 413 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP B 422 " --> pdb=" O TYR B 437 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR B 437 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 424 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 435 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN B 426 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS B 328 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY B 313 " --> pdb=" O CYS B 328 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 368 removed outlier: 6.816A pdb=" N CYS B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 356 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 323 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE B 326 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AC8, first strand: chain 'B' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN B 683 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA B 694 " --> pdb=" O GLN B 683 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 685 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU B 662 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR B 654 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER B 601 " --> pdb=" O LYS B 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY B 603 " --> pdb=" O LYS B 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS B 562 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 514 through 515 removed outlier: 4.183A pdb=" N SER B 589 " --> pdb=" O TRP B 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP B 585 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 581 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA B 595 " --> pdb=" O PHE B 579 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 579 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 597 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS B 577 " --> pdb=" O TYR B 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 727 through 731 removed outlier: 6.775A pdb=" N ILE B 736 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR B 730 " --> pdb=" O PHE B 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 734 " --> pdb=" O THR B 730 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B1133 " --> pdb=" O HIS B1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS B1114 " --> pdb=" O LEU B1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 779 removed outlier: 6.895A pdb=" N ASN B 762 " --> pdb=" O LYS B1142 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B1142 " --> pdb=" O ASN B 762 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER B 764 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1140 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B1138 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN B 768 " --> pdb=" O THR B1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS B1142 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B1164 " --> pdb=" O TRP B1144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 785 through 787 Processing sheet with id=AD7, first strand: chain 'B' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE B1202 " --> pdb=" O CYS B1148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 42 removed outlier: 7.246A pdb=" N THR C 191 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL C 206 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR C 204 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR C 195 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.147A pdb=" N ALA C 99 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR C 133 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 101 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 131 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 103 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN C 129 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 105 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 125 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 156 through 161 removed outlier: 3.719A pdb=" N GLY C 62 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN C 299 " --> pdb=" O TRP C 413 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL C 415 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG C 297 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE C 417 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 295 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE C 384 " --> pdb=" O TYR C 391 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 247 through 262 removed outlier: 5.505A pdb=" N VAL C 248 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 427 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ARG C 250 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 425 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR C 252 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 423 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 421 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 417 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 260 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 415 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP C 413 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP C 422 " --> pdb=" O TYR C 437 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR C 437 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 424 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 435 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN C 426 " --> pdb=" O GLN C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS C 328 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY C 313 " --> pdb=" O CYS C 328 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 360 through 368 removed outlier: 6.817A pdb=" N CYS C 351 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR C 356 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP C 323 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N PHE C 326 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 343 through 344 Processing sheet with id=AE7, first strand: chain 'C' and resid 457 through 461 removed outlier: 6.618A pdb=" N GLN C 683 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C 694 " --> pdb=" O GLN C 683 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 685 " --> pdb=" O ILE C 692 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 471 through 474 removed outlier: 5.032A pdb=" N LEU C 662 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR C 654 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 504 through 509 removed outlier: 6.456A pdb=" N SER C 601 " --> pdb=" O LYS C 564 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY C 603 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS C 562 " --> pdb=" O GLY C 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 514 through 515 removed outlier: 4.184A pdb=" N SER C 589 " --> pdb=" O TRP C 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 585 " --> pdb=" O SER C 589 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 581 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 595 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE C 579 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR C 597 " --> pdb=" O CYS C 577 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS C 577 " --> pdb=" O TYR C 597 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 727 through 731 removed outlier: 6.774A pdb=" N ILE C 736 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR C 730 " --> pdb=" O PHE C 734 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE C 734 " --> pdb=" O THR C 730 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C1133 " --> pdb=" O HIS C1114 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS C1114 " --> pdb=" O LEU C1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 761 through 779 removed outlier: 6.896A pdb=" N ASN C 762 " --> pdb=" O LYS C1142 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C1142 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 764 " --> pdb=" O ASN C1140 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN C1140 " --> pdb=" O SER C 764 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR C1138 " --> pdb=" O PRO C 766 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 768 " --> pdb=" O THR C1136 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS C1142 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C1164 " --> pdb=" O TRP C1144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 785 through 787 Processing sheet with id=AF6, first strand: chain 'C' and resid 1189 through 1191 removed outlier: 4.065A pdb=" N ILE C1202 " --> pdb=" O CYS C1148 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3312 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: 16.83 Time building geometry restraints manager: 16.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7568 1.33 - 1.47: 10479 1.47 - 1.61: 12694 1.61 - 1.75: 36 1.75 - 1.89: 141 Bond restraints: 30918 Sorted by residual: bond pdb=" C VAL B1190 " pdb=" N GLN B1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 9.05e+01 bond pdb=" C VAL C1190 " pdb=" N GLN C1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C VAL A1190 " pdb=" N GLN A1191 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.42e-02 4.96e+03 8.99e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C1 NAG u 2 " pdb=" O5 NAG u 2 " ideal model delta sigma weight residual 1.406 1.580 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 30913 not shown) Histogram of bond angle deviations from ideal: 69.36 - 85.83: 75 85.83 - 102.31: 529 102.31 - 118.78: 24746 118.78 - 135.26: 16758 135.26 - 151.74: 51 Bond angle restraints: 42159 Sorted by residual: angle pdb=" C2 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 107.58 151.74 -44.16 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 107.58 151.73 -44.15 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C2 MAN K 4 " pdb=" C3 MAN K 4 " pdb=" O3 MAN K 4 " ideal model delta sigma weight residual 107.58 151.70 -44.12 3.00e+00 1.11e-01 2.16e+02 angle pdb=" C4 MAN f 4 " pdb=" C3 MAN f 4 " pdb=" O3 MAN f 4 " ideal model delta sigma weight residual 111.95 70.52 41.43 3.00e+00 1.11e-01 1.91e+02 angle pdb=" C4 MAN 0 4 " pdb=" C3 MAN 0 4 " pdb=" O3 MAN 0 4 " ideal model delta sigma weight residual 111.95 70.53 41.42 3.00e+00 1.11e-01 1.91e+02 ... (remaining 42154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 19712 23.75 - 47.50: 823 47.50 - 71.25: 246 71.25 - 95.01: 201 95.01 - 118.76: 78 Dihedral angle restraints: 21060 sinusoidal: 10737 harmonic: 10323 Sorted by residual: dihedral pdb=" C ALA B 810 " pdb=" N ALA B 810 " pdb=" CA ALA B 810 " pdb=" CB ALA B 810 " ideal model delta harmonic sigma weight residual -122.60 -146.41 23.81 0 2.50e+00 1.60e-01 9.07e+01 dihedral pdb=" C ALA C 810 " pdb=" N ALA C 810 " pdb=" CA ALA C 810 " pdb=" CB ALA C 810 " ideal model delta harmonic sigma weight residual -122.60 -146.40 23.80 0 2.50e+00 1.60e-01 9.06e+01 dihedral pdb=" C ALA A 810 " pdb=" N ALA A 810 " pdb=" CA ALA A 810 " pdb=" CB ALA A 810 " ideal model delta harmonic sigma weight residual -122.60 -146.37 23.77 0 2.50e+00 1.60e-01 9.04e+01 ... (remaining 21057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4966 0.264 - 0.528: 385 0.528 - 0.792: 109 0.792 - 1.056: 51 1.056 - 1.320: 27 Chirality restraints: 5538 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG u 2 " pdb=" O4 NAG u 1 " pdb=" C2 NAG u 2 " pdb=" O5 NAG u 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 3.91e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-02 2.50e+03 3.88e+02 ... (remaining 5535 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN B 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 486 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN A 486 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 486 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 486 " -0.157 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 486 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN C 486 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN C 486 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 486 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG 1 1 " -0.120 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 42 2.16 - 2.85: 10971 2.85 - 3.53: 39555 3.53 - 4.22: 74296 4.22 - 4.90: 118793 Nonbonded interactions: 243657 Sorted by model distance: nonbonded pdb=" O4 NAG g 1 " pdb=" C1 NAG g 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG L 1 " pdb=" C1 NAG L 2 " model vdw 1.476 3.470 nonbonded pdb=" O4 NAG 1 1 " pdb=" C1 NAG 1 2 " model vdw 1.476 3.470 nonbonded pdb=" O ASN C1111 " pdb=" OD1 ASN C1111 " model vdw 1.738 3.040 nonbonded pdb=" O ASN A1111 " pdb=" OD1 ASN A1111 " model vdw 1.738 3.040 ... (remaining 243652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'K' selection = chain 'f' } ncs_group { reference = chain '1' selection = chain '4' selection = chain 'DA' selection = chain 'L' selection = chain 'O' selection = chain 'X' selection = chain 'g' selection = chain 'j' selection = chain 's' } ncs_group { reference = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'CA' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'w' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '3' selection = chain 'BA' selection = chain 'N' selection = chain 'V' selection = chain 'i' selection = chain 'q' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'AA' selection = chain 'F' selection = chain 'H' selection = chain 'U' selection = chain 'a' selection = chain 'c' selection = chain 'p' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain 'D' selection = chain 'Y' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.040 Extract box with map and model: 1.240 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 89.140 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.024 0.174 30918 Z= 1.499 Angle : 3.036 44.157 42159 Z= 1.342 Chirality : 0.199 1.320 5538 Planarity : 0.012 0.113 5064 Dihedral : 18.246 118.758 14304 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.70 % Favored : 93.70 % Rotamer: Outliers : 0.68 % Allowed : 1.45 % Favored : 97.87 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3507 helix: 0.72 (0.19), residues: 708 sheet: 0.72 (0.18), residues: 852 loop : -0.95 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.006 TRP A 600 HIS 0.007 0.002 HIS B 542 PHE 0.023 0.005 PHE B 950 TYR 0.037 0.006 TYR C 654 ARG 0.006 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 468 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 VAL cc_start: 0.8463 (t) cc_final: 0.8065 (p) REVERT: A 515 VAL cc_start: 0.8523 (t) cc_final: 0.8288 (p) REVERT: A 851 TYR cc_start: 0.7618 (m-80) cc_final: 0.7016 (m-80) REVERT: A 916 VAL cc_start: 0.8430 (t) cc_final: 0.8002 (t) REVERT: B 153 LEU cc_start: 0.8295 (mt) cc_final: 0.7976 (mt) REVERT: B 362 VAL cc_start: 0.8143 (t) cc_final: 0.7649 (p) REVERT: B 538 ASP cc_start: 0.6525 (m-30) cc_final: 0.6209 (m-30) REVERT: B 916 VAL cc_start: 0.8667 (t) cc_final: 0.8382 (t) REVERT: C 362 VAL cc_start: 0.8268 (t) cc_final: 0.7849 (p) REVERT: C 763 LEU cc_start: 0.9091 (mt) cc_final: 0.8865 (mp) outliers start: 21 outliers final: 13 residues processed: 489 average time/residue: 0.3968 time to fit residues: 301.8897 Evaluate side-chains 185 residues out of total 3093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain A residue 1111 ASN Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 1111 ASN Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 1111 ASN Chi-restraints excluded: chain C residue 1138 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 318 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 ASN C 433 GLN C1021 GLN C1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2408 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: