Starting phenix.real_space_refine on Fri Feb 23 07:56:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/02_2024/7upy_26678_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/02_2024/7upy_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_26678/02_2024/7upy_26678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/02_2024/7upy_26678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/02_2024/7upy_26678_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upy_26678/02_2024/7upy_26678_neut.pdb" } resolution = 3.1 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= 0.024 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 6 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 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 24 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 dihedrals: 24 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 20.62, per 1000 atoms: 0.55 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: 16.46 Conformation dependent library (CDL) restraints added in 6.9 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: 5.02 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: 20.60 Time building geometry restraints manager: 17.09 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 - 24.65: 22875 24.65 - 49.31: 903 49.31 - 73.96: 206 73.96 - 98.61: 71 98.61 - 123.27: 41 Dihedral angle restraints: 24096 sinusoidal: 10682 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 24093 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: 9.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 30.580 Check model and map are aligned: 0.560 Set scattering table: 0.390 Process input model: 107.710 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.490 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.030 ------------------------------------------------------------------------------- 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 : 15.613 123.266 15322 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 % Allowed : 4.94 % Favored : 92.84 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.169 0.020 TRP B 104 HIS 0.020 0.004 HIS B1159 PHE 0.097 0.014 PHE A 718 TYR 0.119 0.019 TYR B 38 ARG 0.009 0.001 ARG C 328 *********************** 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 : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: B 190 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.5643 (ttp-110) REVERT: B 571 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 957 GLN cc_start: 0.8027 (tt0) cc_final: 0.7700 (tp40) REVERT: C 53 ASP cc_start: 0.7783 (t0) cc_final: 0.7545 (t0) REVERT: C 78 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6377 (tpt90) REVERT: C 144 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6613 (t80) REVERT: C 298 GLU cc_start: 0.8183 (tt0) cc_final: 0.7965 (tt0) REVERT: C 420 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: C 856 ASN cc_start: 0.7971 (m110) cc_final: 0.7684 (m110) REVERT: C 936 ASP cc_start: 0.7524 (m-30) cc_final: 0.7235 (m-30) REVERT: H 99 TYR cc_start: 0.7663 (m-80) cc_final: 0.7350 (m-80) REVERT: E 183 LYS cc_start: 0.3972 (tptp) cc_final: 0.3726 (pttt) REVERT: E 190 LYS cc_start: 0.7567 (ttmp) cc_final: 0.7162 (ttpt) outliers start: 89 outliers final: 31 residues processed: 495 average time/residue: 0.5318 time to fit residues: 421.0499 Evaluate side-chains 302 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain G residue 14 SER 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: 0.9990 chunk 118 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 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: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 787 GLN A 907 ASN A 926 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 658 ASN B 675 GLN B 919 ASN B 926 GLN B 955 ASN B1002 GLN C 121 ASN C 580 GLN C 644 GLN C 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN H 61 GLN H 64 GLN L 79 GLN D 52 ASN D 61 GLN D 64 GLN E 189 HIS G 3 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 38141 Z= 0.355 Angle : 0.780 13.187 51904 Z= 0.397 Chirality : 0.052 0.796 6187 Planarity : 0.005 0.074 6551 Dihedral : 12.303 117.088 7271 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.61 % Favored : 96.13 % Rotamer: Outliers : 2.22 % Allowed : 7.93 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.02 % 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: -0.37 (0.12), residues: 4575 helix: 0.43 (0.18), residues: 777 sheet: 0.59 (0.13), residues: 1352 loop : -0.95 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 50 HIS 0.011 0.002 HIS A 207 PHE 0.032 0.002 PHE D 146 TYR 0.036 0.002 TYR A 904 ARG 0.007 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 2 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 388 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 299 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 988 GLU cc_start: 0.7612 (tt0) cc_final: 0.7408 (tp30) REVERT: B 235 ILE cc_start: 0.7026 (mt) cc_final: 0.6819 (mm) REVERT: B 745 ASP cc_start: 0.6491 (t0) cc_final: 0.6216 (t0) REVERT: B 957 GLN cc_start: 0.7990 (tt0) cc_final: 0.7601 (tp-100) REVERT: B 1145 LEU cc_start: 0.7658 (mp) cc_final: 0.7195 (tp) REVERT: C 78 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6410 (tpt90) REVERT: C 144 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6816 (t80) REVERT: C 856 ASN cc_start: 0.8053 (m110) cc_final: 0.7750 (m-40) REVERT: C 988 GLU cc_start: 0.7699 (mp0) cc_final: 0.7487 (mp0) REVERT: H 29 PHE cc_start: 0.7926 (t80) cc_final: 0.7654 (t80) REVERT: H 32 THR cc_start: 0.7525 (p) cc_final: 0.6957 (t) REVERT: L 122 ASP cc_start: 0.6290 (m-30) cc_final: 0.6070 (p0) REVERT: E 183 LYS cc_start: 0.3842 (tptp) cc_final: 0.3306 (ptpt) REVERT: F 48 MET cc_start: 0.1898 (OUTLIER) cc_final: 0.1382 (mmt) REVERT: F 80 MET cc_start: 0.2625 (ttp) cc_final: 0.2263 (ttp) outliers start: 89 outliers final: 53 residues processed: 367 average time/residue: 0.5340 time to fit residues: 316.2190 Evaluate side-chains 308 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 252 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 346 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 416 optimal weight: 30.0000 chunk 450 optimal weight: 6.9990 chunk 371 optimal weight: 0.0270 chunk 413 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 334 optimal weight: 0.0030 overall best weight: 2.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1119 ASN B 437 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 540 ASN C 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS D 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 38141 Z= 0.388 Angle : 0.725 13.496 51904 Z= 0.364 Chirality : 0.050 0.625 6187 Planarity : 0.005 0.055 6551 Dihedral : 11.300 117.934 7228 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.44 % Favored : 95.37 % Rotamer: Outliers : 2.64 % Allowed : 10.48 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.26 (0.12), residues: 4575 helix: 0.97 (0.19), residues: 778 sheet: 0.58 (0.14), residues: 1286 loop : -0.97 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 50 HIS 0.008 0.002 HIS C1058 PHE 0.028 0.002 PHE A 133 TYR 0.024 0.002 TYR L 91 ARG 0.006 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 3 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 379 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 273 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7893 (t0) REVERT: A 461 LEU cc_start: -0.0052 (OUTLIER) cc_final: -0.0499 (tt) REVERT: A 1148 PHE cc_start: 0.5152 (OUTLIER) cc_final: 0.4899 (m-80) REVERT: B 212 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5140 (tt) REVERT: B 235 ILE cc_start: 0.6971 (mt) cc_final: 0.6746 (mm) REVERT: B 324 GLU cc_start: 0.7861 (pm20) cc_final: 0.7638 (pm20) REVERT: B 745 ASP cc_start: 0.6718 (t0) cc_final: 0.6318 (t0) REVERT: B 957 GLN cc_start: 0.7977 (tt0) cc_final: 0.7615 (tp-100) REVERT: B 1145 LEU cc_start: 0.7659 (mp) cc_final: 0.7164 (tp) REVERT: C 78 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6476 (tpt90) REVERT: C 109 THR cc_start: 0.8481 (p) cc_final: 0.8254 (t) REVERT: C 144 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6916 (t80) REVERT: C 856 ASN cc_start: 0.8063 (m110) cc_final: 0.7764 (m110) REVERT: C 1119 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8863 (m-40) REVERT: H 12 LYS cc_start: 0.4460 (mmtm) cc_final: 0.4032 (mptt) REVERT: H 29 PHE cc_start: 0.7900 (t80) cc_final: 0.7615 (t80) REVERT: H 48 MET cc_start: 0.7432 (mtp) cc_final: 0.7084 (mtm) REVERT: L 122 ASP cc_start: 0.6278 (m-30) cc_final: 0.6042 (p0) REVERT: E 183 LYS cc_start: 0.3858 (tptp) cc_final: 0.3324 (ptpt) REVERT: E 207 LYS cc_start: 0.1999 (tttt) cc_final: 0.1072 (tptt) REVERT: F 80 MET cc_start: 0.2673 (ttp) cc_final: 0.2386 (ttp) outliers start: 106 outliers final: 66 residues processed: 362 average time/residue: 0.5176 time to fit residues: 304.8431 Evaluate side-chains 313 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 240 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 20.0000 chunk 313 optimal weight: 0.6980 chunk 216 optimal weight: 0.1980 chunk 46 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 418 optimal weight: 30.0000 chunk 442 optimal weight: 2.9990 chunk 218 optimal weight: 30.0000 chunk 396 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 38141 Z= 0.272 Angle : 0.657 12.758 51904 Z= 0.326 Chirality : 0.047 0.579 6187 Planarity : 0.004 0.047 6551 Dihedral : 10.732 115.686 7218 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 2.62 % Allowed : 11.60 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.09 (0.12), residues: 4575 helix: 1.37 (0.19), residues: 778 sheet: 0.62 (0.14), residues: 1211 loop : -0.87 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 103 HIS 0.005 0.001 HIS D 200 PHE 0.025 0.002 PHE F 63 TYR 0.030 0.002 TYR E 49 ARG 0.005 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 4 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 364 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 259 time to evaluate : 4.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 754 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8543 (mp) REVERT: A 843 ASP cc_start: 0.1888 (OUTLIER) cc_final: 0.1103 (p0) REVERT: A 1149 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5110 (mptt) REVERT: B 212 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5096 (tt) REVERT: B 516 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: B 745 ASP cc_start: 0.6687 (t0) cc_final: 0.6310 (t0) REVERT: B 957 GLN cc_start: 0.7984 (tt0) cc_final: 0.7555 (tp-100) REVERT: B 1145 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7145 (tp) REVERT: C 78 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6386 (tpt90) REVERT: C 144 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7110 (t80) REVERT: C 661 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: C 856 ASN cc_start: 0.8035 (m110) cc_final: 0.7820 (m-40) REVERT: H 12 LYS cc_start: 0.4429 (mmtm) cc_final: 0.4048 (mptt) REVERT: H 29 PHE cc_start: 0.7876 (t80) cc_final: 0.7600 (t80) REVERT: H 48 MET cc_start: 0.7557 (mtp) cc_final: 0.7159 (mtm) REVERT: H 209 LYS cc_start: 0.1142 (ttmm) cc_final: 0.0546 (mmmm) REVERT: L 122 ASP cc_start: 0.6350 (m-30) cc_final: 0.6083 (p0) REVERT: D 201 LYS cc_start: 0.3874 (mmtm) cc_final: 0.3631 (mmmt) REVERT: D 207 VAL cc_start: 0.4122 (OUTLIER) cc_final: 0.3860 (t) REVERT: E 183 LYS cc_start: 0.3693 (tptp) cc_final: 0.3210 (ptpt) REVERT: F 80 MET cc_start: 0.2778 (ttp) cc_final: 0.2262 (ttp) outliers start: 105 outliers final: 60 residues processed: 341 average time/residue: 0.5470 time to fit residues: 308.5391 Evaluate side-chains 314 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 244 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 50.0000 chunk 251 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 182 optimal weight: 0.9990 chunk 377 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 397 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 493 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 38141 Z= 0.394 Angle : 0.701 13.485 51904 Z= 0.347 Chirality : 0.049 0.537 6187 Planarity : 0.004 0.044 6551 Dihedral : 10.406 118.380 7213 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 3.17 % Allowed : 12.28 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.20 (0.12), residues: 4575 helix: 1.31 (0.19), residues: 778 sheet: 0.52 (0.14), residues: 1226 loop : -0.94 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 103 HIS 0.008 0.001 HIS C1058 PHE 0.021 0.002 PHE A 565 TYR 0.022 0.002 TYR L 91 ARG 0.004 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 5 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 397 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 270 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8016 (m-80) cc_final: 0.7804 (m-80) REVERT: A 226 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6904 (tt) REVERT: A 461 LEU cc_start: 0.0274 (OUTLIER) cc_final: -0.0292 (tt) REVERT: A 619 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 843 ASP cc_start: 0.1985 (OUTLIER) cc_final: 0.1193 (p0) REVERT: A 1113 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: A 1149 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5219 (mptt) REVERT: B 212 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.5264 (tt) REVERT: B 516 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: B 745 ASP cc_start: 0.6761 (t0) cc_final: 0.6481 (t0) REVERT: B 957 GLN cc_start: 0.7962 (tt0) cc_final: 0.7604 (tp-100) REVERT: B 995 ARG cc_start: 0.8706 (mtt-85) cc_final: 0.8384 (mtp-110) REVERT: B 1145 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7124 (tp) REVERT: C 78 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6509 (tpt90) REVERT: C 118 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8611 (tp) REVERT: C 144 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7159 (t80) REVERT: C 346 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7228 (mmt90) REVERT: C 856 ASN cc_start: 0.8036 (m110) cc_final: 0.7797 (m-40) REVERT: H 12 LYS cc_start: 0.4603 (mmtm) cc_final: 0.4235 (mptt) REVERT: H 29 PHE cc_start: 0.7835 (t80) cc_final: 0.7561 (t80) REVERT: H 48 MET cc_start: 0.7625 (mtp) cc_final: 0.7288 (mtm) REVERT: H 209 LYS cc_start: 0.1190 (ttmm) cc_final: 0.0958 (mmmm) REVERT: L 122 ASP cc_start: 0.6343 (m-30) cc_final: 0.6056 (p0) REVERT: D 207 VAL cc_start: 0.4075 (OUTLIER) cc_final: 0.3835 (m) REVERT: E 183 LYS cc_start: 0.3797 (tptp) cc_final: 0.3266 (ptpt) REVERT: E 207 LYS cc_start: 0.1426 (tttt) cc_final: 0.0556 (tptt) REVERT: F 19 LYS cc_start: 0.2040 (ttpt) cc_final: 0.1819 (tppt) REVERT: F 80 MET cc_start: 0.2762 (ttp) cc_final: 0.2282 (ttp) outliers start: 127 outliers final: 86 residues processed: 375 average time/residue: 0.4944 time to fit residues: 303.7259 Evaluate side-chains 349 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 251 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 7.9990 chunk 398 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 259 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 443 optimal weight: 20.0000 chunk 367 optimal weight: 0.0050 chunk 205 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 overall best weight: 2.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 38141 Z= 0.339 Angle : 0.664 13.073 51904 Z= 0.328 Chirality : 0.047 0.496 6187 Planarity : 0.004 0.050 6551 Dihedral : 9.994 116.527 7211 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.13 % Favored : 95.72 % Rotamer: Outliers : 3.14 % Allowed : 12.95 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.22 (0.12), residues: 4575 helix: 1.33 (0.19), residues: 783 sheet: 0.52 (0.14), residues: 1208 loop : -0.97 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 103 HIS 0.005 0.001 HIS C1058 PHE 0.018 0.002 PHE A 541 TYR 0.038 0.002 TYR E 49 ARG 0.012 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 6 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 386 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 260 time to evaluate : 4.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.0224 (OUTLIER) cc_final: -0.0329 (tt) REVERT: A 619 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 754 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 1149 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5195 (mptt) REVERT: B 212 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5201 (tt) REVERT: B 516 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: B 745 ASP cc_start: 0.6762 (t0) cc_final: 0.6550 (t0) REVERT: B 957 GLN cc_start: 0.7959 (tt0) cc_final: 0.7648 (tp-100) REVERT: B 995 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.8409 (mtp-110) REVERT: B 1145 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7115 (tp) REVERT: C 78 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6484 (tpt90) REVERT: C 118 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8609 (tp) REVERT: C 144 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7203 (t80) REVERT: C 346 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7270 (mmt90) REVERT: C 661 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: C 856 ASN cc_start: 0.8021 (m110) cc_final: 0.7798 (m-40) REVERT: C 861 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9043 (mt) REVERT: H 48 MET cc_start: 0.7641 (mtp) cc_final: 0.7290 (mtm) REVERT: H 209 LYS cc_start: 0.1506 (ttmm) cc_final: 0.1256 (mmmm) REVERT: L 122 ASP cc_start: 0.6302 (m-30) cc_final: 0.6019 (p0) REVERT: D 197 ASN cc_start: 0.3480 (OUTLIER) cc_final: 0.3188 (t0) REVERT: D 207 VAL cc_start: 0.4066 (OUTLIER) cc_final: 0.3855 (m) REVERT: E 183 LYS cc_start: 0.3789 (tptp) cc_final: 0.3156 (ptpt) REVERT: E 207 LYS cc_start: 0.1424 (tttt) cc_final: 0.0578 (tptt) REVERT: F 19 LYS cc_start: 0.2057 (ttpt) cc_final: 0.1637 (tppt) REVERT: F 80 MET cc_start: 0.2841 (ttp) cc_final: 0.2086 (ttp) REVERT: F 150 VAL cc_start: 0.0203 (OUTLIER) cc_final: -0.0044 (p) outliers start: 126 outliers final: 86 residues processed: 361 average time/residue: 0.5124 time to fit residues: 302.4254 Evaluate side-chains 348 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 248 time to evaluate : 4.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 427 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 373 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 441 optimal weight: 7.9990 chunk 276 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 38141 Z= 0.296 Angle : 0.649 13.071 51904 Z= 0.319 Chirality : 0.046 0.470 6187 Planarity : 0.004 0.045 6551 Dihedral : 9.627 115.309 7211 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.35 % Favored : 95.50 % Rotamer: Outliers : 3.09 % Allowed : 13.32 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.18 (0.12), residues: 4575 helix: 1.40 (0.19), residues: 787 sheet: 0.50 (0.14), residues: 1197 loop : -0.92 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 103 HIS 0.005 0.001 HIS F 200 PHE 0.016 0.002 PHE B 157 TYR 0.021 0.001 TYR L 91 ARG 0.006 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 7 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 381 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 257 time to evaluate : 4.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.0277 (OUTLIER) cc_final: -0.0258 (tt) REVERT: A 619 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7067 (mt-10) REVERT: A 754 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 1113 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: A 1149 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5238 (mptt) REVERT: B 212 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5217 (tt) REVERT: B 516 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: B 957 GLN cc_start: 0.7955 (tt0) cc_final: 0.7642 (tp-100) REVERT: B 1145 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7129 (tp) REVERT: C 78 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6538 (tpt90) REVERT: C 118 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8611 (tp) REVERT: C 144 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7208 (t80) REVERT: C 464 PHE cc_start: 0.8785 (m-80) cc_final: 0.8486 (m-80) REVERT: C 661 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: C 808 ASP cc_start: 0.6597 (OUTLIER) cc_final: 0.6172 (m-30) REVERT: C 856 ASN cc_start: 0.8006 (m110) cc_final: 0.7793 (m-40) REVERT: H 48 MET cc_start: 0.7645 (mtp) cc_final: 0.7335 (mtm) REVERT: L 4 MET cc_start: 0.6812 (ttp) cc_final: 0.6232 (ttp) REVERT: L 122 ASP cc_start: 0.6380 (m-30) cc_final: 0.6053 (p0) REVERT: L 183 LYS cc_start: 0.1565 (mmmt) cc_final: 0.1112 (mmmm) REVERT: D 197 ASN cc_start: 0.3454 (OUTLIER) cc_final: 0.3191 (t0) REVERT: D 207 VAL cc_start: 0.4106 (OUTLIER) cc_final: 0.3894 (m) REVERT: E 183 LYS cc_start: 0.3735 (tptp) cc_final: 0.3102 (ptpt) REVERT: E 207 LYS cc_start: 0.1370 (tttt) cc_final: 0.0538 (tptt) REVERT: F 19 LYS cc_start: 0.2102 (ttpt) cc_final: 0.1699 (tppt) REVERT: F 80 MET cc_start: 0.2844 (ttp) cc_final: 0.2068 (ttp) REVERT: F 150 VAL cc_start: -0.0118 (OUTLIER) cc_final: -0.0456 (p) outliers start: 124 outliers final: 93 residues processed: 357 average time/residue: 0.5469 time to fit residues: 325.4765 Evaluate side-chains 349 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 241 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 8.9990 chunk 176 optimal weight: 0.5980 chunk 263 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 280 optimal weight: 3.9990 chunk 300 optimal weight: 0.9980 chunk 218 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 346 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 38141 Z= 0.186 Angle : 0.604 12.546 51904 Z= 0.295 Chirality : 0.044 0.458 6187 Planarity : 0.004 0.044 6551 Dihedral : 9.069 112.086 7211 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Rotamer: Outliers : 2.64 % Allowed : 13.95 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.05 (0.12), residues: 4575 helix: 1.64 (0.19), residues: 786 sheet: 0.54 (0.14), residues: 1203 loop : -0.86 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 103 HIS 0.006 0.001 HIS B 519 PHE 0.024 0.001 PHE A 133 TYR 0.020 0.001 TYR D 27 ARG 0.006 0.000 ARG D 82B *********************** REFINEMENT MACRO_CYCLE 8 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 376 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 270 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8001 (p90) cc_final: 0.7703 (p90) REVERT: A 461 LEU cc_start: 0.0368 (OUTLIER) cc_final: -0.0234 (tt) REVERT: A 619 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 754 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 1149 LYS cc_start: 0.6148 (OUTLIER) cc_final: 0.5204 (mptt) REVERT: B 212 LEU cc_start: 0.5455 (OUTLIER) cc_final: 0.5109 (tt) REVERT: B 516 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: B 957 GLN cc_start: 0.7956 (tt0) cc_final: 0.7629 (tp-100) REVERT: C 78 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6493 (tpt90) REVERT: C 144 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7208 (t80) REVERT: C 464 PHE cc_start: 0.8775 (m-80) cc_final: 0.8462 (m-80) REVERT: C 808 ASP cc_start: 0.6381 (OUTLIER) cc_final: 0.6126 (m-30) REVERT: C 861 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9021 (mt) REVERT: H 48 MET cc_start: 0.7582 (mtp) cc_final: 0.7323 (mtm) REVERT: L 122 ASP cc_start: 0.6324 (m-30) cc_final: 0.6018 (p0) REVERT: L 183 LYS cc_start: 0.1517 (mmmt) cc_final: 0.1161 (mmmm) REVERT: L 190 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7266 (tptp) REVERT: D 207 VAL cc_start: 0.4077 (OUTLIER) cc_final: 0.3847 (m) REVERT: E 183 LYS cc_start: 0.3743 (tptp) cc_final: 0.3085 (ptpt) REVERT: E 207 LYS cc_start: 0.1617 (tttt) cc_final: 0.0774 (tptt) REVERT: F 19 LYS cc_start: 0.1999 (ttpt) cc_final: 0.1652 (tppt) REVERT: F 80 MET cc_start: 0.2545 (ttp) cc_final: 0.1969 (ttp) REVERT: F 150 VAL cc_start: -0.0156 (OUTLIER) cc_final: -0.0473 (p) outliers start: 106 outliers final: 70 residues processed: 356 average time/residue: 0.5033 time to fit residues: 294.8645 Evaluate side-chains 335 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 254 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 401 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 385 optimal weight: 20.0000 chunk 411 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 323 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 371 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 409 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1005 GLN A1135 ASN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.132 38141 Z= 0.664 Angle : 0.813 13.982 51904 Z= 0.404 Chirality : 0.055 0.456 6187 Planarity : 0.005 0.048 6551 Dihedral : 9.785 120.058 7211 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 2.67 % Allowed : 14.07 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4575 helix: 0.96 (0.19), residues: 772 sheet: 0.16 (0.14), residues: 1276 loop : -1.03 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 50 HIS 0.010 0.002 HIS C1058 PHE 0.038 0.003 PHE A 133 TYR 0.027 0.003 TYR L 91 ARG 0.007 0.001 ARG D 82B *********************** REFINEMENT MACRO_CYCLE 9 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 354 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 247 time to evaluate : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.0414 (OUTLIER) cc_final: -0.0165 (tt) REVERT: A 619 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 754 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 1113 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: A 1149 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5126 (mptt) REVERT: B 516 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: B 957 GLN cc_start: 0.7973 (tt0) cc_final: 0.7617 (tp-100) REVERT: C 78 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6610 (tpt90) REVERT: C 144 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7289 (t80) REVERT: C 464 PHE cc_start: 0.8848 (m-80) cc_final: 0.8555 (m-80) REVERT: C 661 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: C 861 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9064 (mt) REVERT: H 29 PHE cc_start: 0.7821 (t80) cc_final: 0.7569 (t80) REVERT: L 122 ASP cc_start: 0.6413 (m-30) cc_final: 0.6022 (p0) REVERT: L 183 LYS cc_start: 0.1727 (mmmt) cc_final: 0.1123 (mmmm) REVERT: D 197 ASN cc_start: 0.3588 (OUTLIER) cc_final: 0.3091 (t0) REVERT: D 207 VAL cc_start: 0.4174 (OUTLIER) cc_final: 0.3957 (m) REVERT: E 145 LYS cc_start: 0.1607 (pttt) cc_final: 0.1368 (ttmm) REVERT: E 183 LYS cc_start: 0.3949 (tptp) cc_final: 0.3135 (ptpt) REVERT: E 207 LYS cc_start: 0.1434 (tttt) cc_final: 0.0577 (tptt) REVERT: F 19 LYS cc_start: 0.1974 (ttpt) cc_final: 0.1636 (tppt) REVERT: F 150 VAL cc_start: 0.0053 (OUTLIER) cc_final: -0.0364 (p) outliers start: 107 outliers final: 81 residues processed: 337 average time/residue: 0.5227 time to fit residues: 290.7064 Evaluate side-chains 335 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 242 time to evaluate : 4.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 270 optimal weight: 1.9990 chunk 434 optimal weight: 40.0000 chunk 265 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 302 optimal weight: 0.7980 chunk 456 optimal weight: 30.0000 chunk 419 optimal weight: 30.0000 chunk 363 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1119 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 38141 Z= 0.240 Angle : 0.633 12.478 51904 Z= 0.312 Chirality : 0.046 0.439 6187 Planarity : 0.004 0.085 6551 Dihedral : 9.070 113.190 7209 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 2.25 % Allowed : 14.57 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4575 helix: 1.38 (0.19), residues: 787 sheet: 0.32 (0.14), residues: 1220 loop : -0.95 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 103 HIS 0.007 0.001 HIS B 519 PHE 0.034 0.001 PHE A 133 TYR 0.021 0.001 TYR D 27 ARG 0.007 0.000 ARG D 94 ********************** REFINEMENT MACRO_CYCLE 10 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 350 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 260 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.0408 (OUTLIER) cc_final: -0.0189 (tt) REVERT: A 619 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7095 (mt-10) REVERT: A 646 ARG cc_start: 0.8348 (mpp80) cc_final: 0.7962 (ttt-90) REVERT: A 754 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8519 (mp) REVERT: A 1149 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5202 (mptt) REVERT: B 471 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 516 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: B 957 GLN cc_start: 0.7923 (tt0) cc_final: 0.7570 (tp-100) REVERT: C 78 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6514 (tpt90) REVERT: C 144 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7260 (t80) REVERT: C 464 PHE cc_start: 0.8861 (m-80) cc_final: 0.8607 (m-80) REVERT: C 567 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7281 (mtm-85) REVERT: C 861 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9029 (mt) REVERT: L 122 ASP cc_start: 0.6299 (m-30) cc_final: 0.5932 (p0) REVERT: L 183 LYS cc_start: 0.1695 (mmmt) cc_final: 0.1128 (mmmm) REVERT: D 197 ASN cc_start: 0.3476 (OUTLIER) cc_final: 0.3141 (t0) REVERT: D 201 LYS cc_start: 0.3946 (mmtm) cc_final: 0.3521 (mmmt) REVERT: E 183 LYS cc_start: 0.3797 (tptp) cc_final: 0.2984 (ptpt) REVERT: E 207 LYS cc_start: 0.1391 (tttt) cc_final: 0.0575 (tptt) REVERT: F 19 LYS cc_start: 0.1903 (ttpt) cc_final: 0.1602 (tppt) REVERT: F 80 MET cc_start: 0.2303 (ttp) cc_final: 0.1903 (ttp) REVERT: F 150 VAL cc_start: 0.0019 (OUTLIER) cc_final: -0.0372 (p) outliers start: 90 outliers final: 70 residues processed: 331 average time/residue: 0.5485 time to fit residues: 292.0316 Evaluate side-chains 334 residues out of total 4017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 254 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1149 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 197 ASN Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 288 optimal weight: 1.9990 chunk 387 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 363 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 373 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.219739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176907 restraints weight = 49293.063| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 5.68 r_work: 0.3472 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 38141 Z= 0.326 Angle : 0.662 13.228 51904 Z= 0.326 Chirality : 0.047 0.440 6187 Planarity : 0.004 0.070 6551 Dihedral : 8.894 114.523 7209 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 2.35 % Allowed : 14.57 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.28 (0.12), residues: 4575 helix: 1.44 (0.19), residues: 784 sheet: 0.30 (0.14), residues: 1220 loop : -0.96 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.007 0.001 HIS B 519 PHE 0.035 0.002 PHE A 133 TYR 0.021 0.002 TYR L 91 ARG 0.005 0.000 ARG D 82B Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8449.05 seconds wall clock time: 157 minutes 13.91 seconds (9433.91 seconds total)