Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/05_2023/7upy_26678_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/05_2023/7upy_26678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/05_2023/7upy_26678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/05_2023/7upy_26678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/05_2023/7upy_26678_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/05_2023/7upy_26678_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 153 5.16 5 C 23602 2.51 5 N 6075 2.21 5 O 7482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 28": "OD1" <-> "OD2" Residue "L ASP 31": "OD1" <-> "OD2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 213": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 161": "OE1" <-> "OE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G ASP 31": "OD1" <-> "OD2" Residue "G ASP 70": "OD1" <-> "OD2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37312 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 8665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8665 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 52, 'TRANS': 1056} Chain breaks: 4 Chain: "B" Number of atoms: 8534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8534 Classifications: {'peptide': 1090} Link IDs: {'PTRANS': 52, 'TRANS': 1037} Chain breaks: 5 Chain: "C" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8678 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 53, 'TRANS': 1055} Chain breaks: 4 Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 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 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 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 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 chiralities: 2 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 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 chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 7 Time building chain proxies: 19.75, per 1000 atoms: 0.53 Number of scatterers: 37312 At special positions: 0 Unit cell: (180.94, 184.26, 247.34, 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 153 16.00 O 7482 8.00 N 6075 7.00 C 23602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM37240 O5 NAG C1402 .*. O " rejected from bonding due to valence issues. Atom "HETATM37044 O5 NAG A1404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG T 2 " - " MAN T 3 " " NAG V 2 " - " MAN V 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG n 2 " - " MAN n 3 " " NAG o 2 " - " MAN o 3 " " NAG q 2 " - " MAN q 3 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG a 1 " - " FUC a 3 " " NAG d 1 " - " FUC d 3 " " NAG m 1 " - " FUC m 3 " " NAG p 1 " - " FUC p 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 234 " " NAG A1404 " - " ASN A 282 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 616 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN A 343 " " NAG T 1 " - " ASN A 165 " " NAG U 1 " - " ASN B 17 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 282 " " NAG X 1 " - " ASN B 616 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B1074 " " NAG b 1 " - " ASN B1098 " " NAG c 1 " - " ASN B1134 " " NAG d 1 " - " ASN B 343 " " NAG e 1 " - " ASN B 165 " " NAG f 1 " - " ASN C 17 " " NAG g 1 " - " ASN C 122 " " NAG h 1 " - " ASN C 234 " " NAG i 1 " - " ASN C 282 " " NAG j 1 " - " ASN C 616 " " NAG k 1 " - " ASN C 717 " " NAG l 1 " - " ASN C 801 " " NAG m 1 " - " ASN C1074 " " NAG n 1 " - " ASN C1098 " " NAG o 1 " - " ASN C1134 " " NAG p 1 " - " ASN C 343 " " NAG q 1 " - " ASN C 165 " Time building additional restraints: 15.13 Conformation dependent library (CDL) restraints added in 7.4 seconds 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8612 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 78 sheets defined 21.6% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.273A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.988A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.629A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.669A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.983A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.646A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.777A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.149A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.899A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.049A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.258A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.562A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.538A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.385A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.699A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.623A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.639A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.786A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.908A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.897A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.989A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.808A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.171A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.721A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 628 Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.878A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.555A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.908A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.510A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.884A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.690A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.025A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 191 removed outlier: 3.989A pdb=" N GLY H 190 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 188' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.990A pdb=" N GLY D 190 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 188' Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.990A pdb=" N GLY F 190 " --> pdb=" O SER F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 183 through 188 removed outlier: 3.652A pdb=" N GLU G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 183 through 188' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.928A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.349A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.182A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.858A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.195A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.570A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.723A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.523A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.876A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.870A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.171A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.507A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.520A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.624A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.288A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.765A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.817A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.627A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.627A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.700A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.525A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.779A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.891A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.422A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.482A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.515A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.587A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.940A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.747A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.043A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.953A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.431A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.003A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.852A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.399A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.212A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.525A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.263A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AG7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.525A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.965A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR D 194 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.524A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 120 through 124 removed outlier: 5.966A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 120 through 124 removed outlier: 5.966A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 151 through 154 removed outlier: 4.205A pdb=" N TYR F 194 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 4 through 6 removed outlier: 4.317A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER G 67 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 114 through 118 removed outlier: 6.411A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 153 through 154 1597 hydrogen bonds defined for protein. 4245 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: 21.97 Time building geometry restraints manager: 17.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6108 1.30 - 1.43: 10210 1.43 - 1.56: 21626 1.56 - 1.69: 5 1.69 - 1.82: 192 Bond restraints: 38141 Sorted by residual: bond pdb=" C TYR F 145 " pdb=" O TYR F 145 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.22e-02 6.72e+03 2.50e+01 bond pdb=" C TYR H 145 " pdb=" O TYR H 145 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.22e-02 6.72e+03 2.49e+01 bond pdb=" C ARG C1014 " pdb=" O ARG C1014 " ideal model delta sigma weight residual 1.237 1.185 0.051 1.19e-02 7.06e+03 1.86e+01 bond pdb=" C1 MAN q 3 " pdb=" O5 MAN q 3 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CA ARG C 355 " pdb=" C ARG C 355 " ideal model delta sigma weight residual 1.522 1.568 -0.046 1.14e-02 7.69e+03 1.65e+01 ... (remaining 38136 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.38: 756 105.38 - 112.97: 18511 112.97 - 120.56: 19271 120.56 - 128.15: 13182 128.15 - 135.74: 184 Bond angle restraints: 51904 Sorted by residual: angle pdb=" C GLU D 148 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " ideal model delta sigma weight residual 119.84 133.05 -13.21 1.25e+00 6.40e-01 1.12e+02 angle pdb=" C GLU H 148 " pdb=" N PRO H 149 " pdb=" CA PRO H 149 " ideal model delta sigma weight residual 119.84 133.04 -13.20 1.25e+00 6.40e-01 1.12e+02 angle pdb=" C GLU F 148 " pdb=" N PRO F 149 " pdb=" CA PRO F 149 " ideal model delta sigma weight residual 119.84 132.99 -13.15 1.25e+00 6.40e-01 1.11e+02 angle pdb=" N ASP B 467 " pdb=" CA ASP B 467 " pdb=" C ASP B 467 " ideal model delta sigma weight residual 108.23 123.60 -15.37 1.72e+00 3.38e-01 7.98e+01 angle pdb=" CA ASN C 125 " pdb=" CB ASN C 125 " pdb=" CG ASN C 125 " ideal model delta sigma weight residual 112.60 120.48 -7.88 1.00e+00 1.00e+00 6.21e+01 ... (remaining 51899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20153 17.99 - 35.98: 1311 35.98 - 53.96: 238 53.96 - 71.95: 104 71.95 - 89.94: 49 Dihedral angle restraints: 21855 sinusoidal: 8441 harmonic: 13414 Sorted by residual: dihedral pdb=" C ASP B 467 " pdb=" N ASP B 467 " pdb=" CA ASP B 467 " pdb=" CB ASP B 467 " ideal model delta harmonic sigma weight residual -122.60 -149.94 27.34 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" N ASP B 467 " pdb=" C ASP B 467 " pdb=" CA ASP B 467 " pdb=" CB ASP B 467 " ideal model delta harmonic sigma weight residual 122.80 149.58 -26.78 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -164.68 78.68 1 1.00e+01 1.00e-02 7.71e+01 ... (remaining 21852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 5986 0.228 - 0.456: 181 0.456 - 0.684: 11 0.684 - 0.911: 4 0.911 - 1.139: 5 Chirality restraints: 6187 Sorted by residual: chirality pdb=" C1 FUC m 3 " pdb=" O6 NAG m 1 " pdb=" C2 FUC m 3 " pdb=" O5 FUC m 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.91e+01 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.46e+01 ... (remaining 6184 not shown) Planarity restraints: 6608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.219 2.00e-02 2.50e+03 2.62e-01 8.56e+02 pdb=" CG ASN B 61 " -0.144 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.418 2.00e-02 2.50e+03 pdb=" C1 NAG B1401 " 0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.198 2.00e-02 2.50e+03 2.20e-01 6.07e+02 pdb=" CG ASN A 61 " -0.132 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.345 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 104 " 0.169 2.00e-02 2.50e+03 9.02e-02 2.03e+02 pdb=" CG TRP B 104 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP B 104 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 104 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP B 104 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TRP B 104 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 104 " -0.132 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 104 " 0.096 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 104 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 104 " 0.111 2.00e-02 2.50e+03 ... (remaining 6605 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 23 2.33 - 2.97: 16700 2.97 - 3.61: 50354 3.61 - 4.26: 87105 4.26 - 4.90: 144505 Nonbonded interactions: 298687 Sorted by model distance: nonbonded pdb=" O VAL B 620 " pdb=" NH2 ARG B 634 " model vdw 1.682 2.520 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 1.693 2.440 nonbonded pdb=" NH2 ARG B 346 " pdb=" OD1 ASP H 95 " model vdw 1.876 2.520 nonbonded pdb=" NH2 ARG B 454 " pdb=" O SER B 469 " model vdw 2.015 2.520 nonbonded pdb=" CD ARG B1107 " pdb=" CE1 TYR C 904 " model vdw 2.090 3.740 ... (remaining 298682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 68 or resid 77 through 829 or resid 853 through \ 1162 or resid 1401 through 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 1162 or resid 1401 thr \ ough 1407)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 623 or resid 636 through \ 829 or resid 853 through 1162 or resid 1401 through 1407)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) } 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: 6.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 29.830 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 102.520 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.014 0.082 38141 Z= 0.902 Angle : 1.857 15.366 51904 Z= 1.219 Chirality : 0.110 1.139 6187 Planarity : 0.012 0.125 6551 Dihedral : 14.001 89.940 13081 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.94 % Allowed : 5.70 % Favored : 93.36 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.39 % 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: -1.19 (0.11), residues: 4575 helix: -1.64 (0.15), residues: 770 sheet: 0.36 (0.14), residues: 1231 loop : -1.09 (0.11), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9150 Ramachandran restraints generated. 4575 Oldfield, 0 Emsley, 4575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 421 time to evaluate : 5.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 31 residues processed: 495 average time/residue: 0.4958 time to fit residues: 395.8280 Evaluate side-chains 294 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 263 time to evaluate : 3.167 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4088 time to fit residues: 26.2659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 9.9990 chunk 347 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 358 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 415 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: