Starting phenix.real_space_refine on Thu Feb 22 10:26:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9o_31034/02_2024/7e9o_31034.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9o_31034/02_2024/7e9o_31034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9o_31034/02_2024/7e9o_31034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9o_31034/02_2024/7e9o_31034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9o_31034/02_2024/7e9o_31034.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9o_31034/02_2024/7e9o_31034.pdb" } resolution = 3.41 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= 1.000 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 147 5.16 5 C 21504 2.51 5 N 5622 2.21 5 O 6603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 192": "OE1" <-> "OE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 148": "OE1" <-> "OE2" Residue "O TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 190": "OD1" <-> "OD2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 118": "OD1" <-> "OD2" Residue "P GLU 165": "OE1" <-> "OE2" Residue "X TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 86": "OE1" <-> "OE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 166": "OE1" <-> "OE2" Residue "X TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 101": "OE1" <-> "OE2" Residue "Y GLU 114": "OE1" <-> "OE2" Residue "Y TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 118": "OD1" <-> "OD2" Residue "Y GLU 165": "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: 33876 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "O" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "P" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "X" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "Y" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.97, per 1000 atoms: 0.53 Number of scatterers: 33876 At special positions: 0 Unit cell: (203.67, 199.29, 226.665, 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 147 16.00 O 6603 8.00 N 5622 7.00 C 21504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 199 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 157 " - pdb=" SG CYS P 213 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS X 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 157 " - pdb=" SG CYS Y 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " Time building additional restraints: 11.75 Conformation dependent library (CDL) restraints added in 5.8 seconds 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 75 sheets defined 19.3% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.316A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.558A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.708A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 4.080A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.569A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.302A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.444A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.011A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.932A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.329A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.076A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.541A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.789A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.918A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.663A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.523A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.708A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.583A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.187A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.772A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.942A pdb=" N GLY C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.524A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.707A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.714A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.943A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.625A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.914A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.501A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.602A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.574A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.405A 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 removed outlier: 3.599A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.473A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.155A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.048A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 4.061A pdb=" N LYS L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 132' Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.915A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'O' and resid 84 through 88 removed outlier: 4.192A pdb=" N VAL O 88 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 131 Processing helix chain 'O' and resid 187 through 194 removed outlier: 3.582A pdb=" N LYS O 193 " --> pdb=" O ALA O 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'P' and resid 173 through 175 No H-bonds generated for 'chain 'P' and resid 173 through 175' Processing helix chain 'P' and resid 202 through 206 removed outlier: 3.625A pdb=" N LEU P 206 " --> pdb=" O SER P 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 88 removed outlier: 3.624A pdb=" N VAL X 88 " --> pdb=" O ALA X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 133 Processing helix chain 'X' and resid 187 through 194 Processing helix chain 'Y' and resid 173 through 175 No H-bonds generated for 'chain 'Y' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.773A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171 removed outlier: 4.134A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.419A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.670A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.605A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.160A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AB4, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.577A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AB6, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.192A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.833A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.040A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.171A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.982A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AD3, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.625A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.142A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.828A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.877A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.359A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.550A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.943A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.061A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1098 removed outlier: 3.921A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.585A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 119 through 123 removed outlier: 6.206A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 158 through 159 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 57 through 60 removed outlier: 7.148A pdb=" N GLY H 50 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR H 60 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL H 48 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 137 through 141 Processing sheet with id=AG1, first strand: chain 'H' and resid 137 through 141 removed outlier: 4.038A pdb=" N SER H 194 " --> pdb=" O VAL H 186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 168 through 171 removed outlier: 4.321A pdb=" N TYR H 211 " --> pdb=" O VAL H 228 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'O' and resid 58 through 59 removed outlier: 6.331A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TYR O 54 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU O 38 " --> pdb=" O TYR O 54 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 119 through 123 removed outlier: 5.817A pdb=" N TYR O 178 " --> pdb=" O ASN O 143 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 158 through 160 removed outlier: 4.352A pdb=" N TRP O 153 " --> pdb=" O GLN O 160 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'P' and resid 46 through 51 removed outlier: 5.092A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS P 98 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL P 119 " --> pdb=" O LYS P 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 137 through 141 Processing sheet with id=AH1, first strand: chain 'P' and resid 137 through 141 Processing sheet with id=AH2, first strand: chain 'P' and resid 168 through 171 Processing sheet with id=AH3, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AH4, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.630A pdb=" N LEU X 11 " --> pdb=" O LYS X 108 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP X 110 " --> pdb=" O LEU X 11 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 119 through 123 removed outlier: 4.129A pdb=" N ASN X 143 " --> pdb=" O TYR X 178 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR X 178 " --> pdb=" O ASN X 143 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER X 179 " --> pdb=" O THR X 169 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 158 through 160 removed outlier: 4.386A pdb=" N TRP X 153 " --> pdb=" O GLN X 160 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AH8, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'Y' and resid 45 through 51 removed outlier: 6.632A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Y' and resid 137 through 141 Processing sheet with id=AI2, first strand: chain 'Y' and resid 137 through 141 Processing sheet with id=AI3, first strand: chain 'Y' and resid 168 through 171 removed outlier: 4.326A pdb=" N TYR Y 211 " --> pdb=" O VAL Y 228 " (cutoff:3.500A) 1372 hydrogen bonds defined for protein. 3648 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: 18.53 Time building geometry restraints manager: 12.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5564 1.31 - 1.44: 9451 1.44 - 1.57: 19437 1.57 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 34641 Sorted by residual: bond pdb=" C7 NAG C1303 " pdb=" N2 NAG C1303 " ideal model delta sigma weight residual 1.346 1.466 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 NAG B1304 " pdb=" N2 NAG B1304 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 NAG A1306 " pdb=" N2 NAG A1306 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.02: 912 106.02 - 113.10: 18721 113.10 - 120.18: 12032 120.18 - 127.26: 15182 127.26 - 134.34: 301 Bond angle restraints: 47148 Sorted by residual: angle pdb=" N ILE A 909 " pdb=" CA ILE A 909 " pdb=" C ILE A 909 " ideal model delta sigma weight residual 111.88 102.35 9.53 1.06e+00 8.90e-01 8.08e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" C PRO C 942 " ideal model delta sigma weight residual 113.40 123.72 -10.32 1.34e+00 5.57e-01 5.94e+01 angle pdb=" C PHE B 906 " pdb=" CA PHE B 906 " pdb=" CB PHE B 906 " ideal model delta sigma weight residual 110.90 100.49 10.41 1.58e+00 4.01e-01 4.34e+01 angle pdb=" CA PHE A 888 " pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" C PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 111.46 103.53 7.93 1.29e+00 6.01e-01 3.78e+01 ... (remaining 47143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 19848 24.09 - 48.18: 895 48.18 - 72.27: 150 72.27 - 96.36: 55 96.36 - 120.45: 79 Dihedral angle restraints: 21027 sinusoidal: 8475 harmonic: 12552 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.95 -90.05 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.07 86.07 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.23 82.23 1 1.00e+01 1.00e-02 8.30e+01 ... (remaining 21024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4999 0.093 - 0.187: 404 0.187 - 0.280: 25 0.280 - 0.374: 2 0.374 - 0.467: 3 Chirality restraints: 5433 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA PHE B 898 " pdb=" N PHE B 898 " pdb=" C PHE B 898 " pdb=" CB PHE B 898 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 5430 not shown) Planarity restraints: 6099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 897 " 0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO B 897 " -0.071 2.00e-02 2.50e+03 pdb=" O PRO B 897 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE B 898 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 740 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C MET B 740 " -0.061 2.00e-02 2.50e+03 pdb=" O MET B 740 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR B 741 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 887 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C THR B 887 " -0.056 2.00e-02 2.50e+03 pdb=" O THR B 887 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE B 888 " 0.019 2.00e-02 2.50e+03 ... (remaining 6096 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2777 2.74 - 3.28: 33288 3.28 - 3.82: 52847 3.82 - 4.36: 61784 4.36 - 4.90: 108254 Nonbonded interactions: 258950 Sorted by model distance: nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.202 2.520 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.206 2.440 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.208 2.440 nonbonded pdb=" OD1 ASN A 282 " pdb=" O3 NAG A1301 " model vdw 2.221 2.440 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.222 2.520 ... (remaining 258945 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 9.870 Check model and map are aligned: 0.560 Set scattering table: 0.320 Process input model: 94.230 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.400 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: 0.020 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.007 0.120 34641 Z= 0.431 Angle : 0.820 10.414 47148 Z= 0.472 Chirality : 0.052 0.467 5433 Planarity : 0.005 0.072 6072 Dihedral : 16.683 120.447 12816 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.24 % Allowed : 0.80 % Favored : 98.96 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.33 % 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: -1.55 (0.12), residues: 4266 helix: 0.47 (0.20), residues: 657 sheet: -0.40 (0.15), residues: 1194 loop : -1.85 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.006 0.001 HIS A1048 PHE 0.036 0.002 PHE A 888 TYR 0.021 0.001 TYR H 211 ARG 0.008 0.001 ARG Y 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 342 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6116 (tp) cc_final: 0.5800 (pt) REVERT: B 740 MET cc_start: 0.8076 (mmt) cc_final: 0.7741 (mmm) REVERT: B 823 PHE cc_start: 0.7491 (m-80) cc_final: 0.7272 (m-80) REVERT: B 902 MET cc_start: 0.8350 (tpt) cc_final: 0.8075 (mmt) REVERT: B 950 ASP cc_start: 0.8412 (p0) cc_final: 0.8106 (p0) REVERT: A 129 LYS cc_start: 0.7191 (tmtt) cc_final: 0.6727 (tptp) REVERT: A 237 ARG cc_start: 0.7839 (ptm-80) cc_final: 0.7525 (mtp-110) REVERT: A 399 SER cc_start: 0.6735 (m) cc_final: 0.6517 (m) REVERT: A 400 PHE cc_start: 0.7566 (p90) cc_final: 0.7226 (p90) REVERT: A 1001 LEU cc_start: 0.8444 (pp) cc_final: 0.8205 (tp) REVERT: A 1142 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7503 (tt0) REVERT: C 215 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6327 (t70) REVERT: C 287 ASP cc_start: 0.7961 (t0) cc_final: 0.7360 (m-30) REVERT: C 740 MET cc_start: 0.8530 (tpt) cc_final: 0.8172 (mtt) REVERT: H 30 ASP cc_start: 0.7664 (m-30) cc_final: 0.7180 (m-30) REVERT: H 60 TYR cc_start: 0.5903 (m-80) cc_final: 0.5636 (m-80) REVERT: O 94 MET cc_start: 0.4423 (tmm) cc_final: 0.4019 (tmm) REVERT: P 39 GLN cc_start: 0.6466 (tm-30) cc_final: 0.6253 (tt0) REVERT: P 46 GLU cc_start: 0.4539 (mm-30) cc_final: 0.4312 (pp20) REVERT: P 65 LYS cc_start: 0.3520 (tttt) cc_final: 0.2428 (mttt) REVERT: P 98 LYS cc_start: 0.3970 (ptmt) cc_final: 0.3359 (mmtp) REVERT: P 102 MET cc_start: 0.6825 (ppp) cc_final: 0.5352 (mpp) REVERT: P 132 SER cc_start: 0.5232 (OUTLIER) cc_final: 0.5002 (t) REVERT: X 31 HIS cc_start: 0.6544 (t70) cc_final: 0.6092 (t-90) REVERT: X 101 PHE cc_start: 0.7332 (m-10) cc_final: 0.7073 (m-10) REVERT: Y 31 ASP cc_start: 0.8754 (m-30) cc_final: 0.8534 (t70) REVERT: Y 227 LYS cc_start: 0.3225 (tmtt) cc_final: 0.2773 (ttmt) outliers start: 9 outliers final: 1 residues processed: 349 average time/residue: 0.4541 time to fit residues: 263.2070 Evaluate side-chains 218 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 6.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Y residue 201 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 336 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 389 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 751 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS L 58 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 HIS ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.162 34641 Z= 0.426 Angle : 0.735 9.517 47148 Z= 0.372 Chirality : 0.051 0.292 5433 Planarity : 0.005 0.061 6072 Dihedral : 12.830 103.005 5200 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.85 % Allowed : 8.17 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.42 (0.12), residues: 4266 helix: 0.88 (0.20), residues: 646 sheet: -0.39 (0.15), residues: 1172 loop : -1.81 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 40 HIS 0.010 0.001 HIS C1058 PHE 0.032 0.002 PHE B 168 TYR 0.027 0.002 TYR A1067 ARG 0.013 0.001 ARG P 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6008 (tp) cc_final: 0.5744 (pt) REVERT: B 823 PHE cc_start: 0.7636 (m-80) cc_final: 0.7391 (m-80) REVERT: B 902 MET cc_start: 0.8436 (tpt) cc_final: 0.8224 (tpp) REVERT: B 981 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 237 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7478 (mtp-110) REVERT: A 399 SER cc_start: 0.6774 (m) cc_final: 0.6506 (m) REVERT: A 400 PHE cc_start: 0.7599 (p90) cc_final: 0.7181 (p90) REVERT: A 957 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7531 (mt0) REVERT: A 1142 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7519 (tt0) REVERT: C 287 ASP cc_start: 0.8003 (t0) cc_final: 0.7284 (m-30) REVERT: C 740 MET cc_start: 0.8554 (tpt) cc_final: 0.8097 (mtt) REVERT: C 1114 ILE cc_start: 0.8835 (tp) cc_final: 0.8578 (mt) REVERT: L 123 PHE cc_start: 0.4071 (m-80) cc_final: 0.3784 (m-80) REVERT: L 178 TYR cc_start: 0.5689 (m-10) cc_final: 0.5059 (m-10) REVERT: H 32 TYR cc_start: 0.6449 (m-80) cc_final: 0.5684 (m-10) REVERT: H 102 MET cc_start: 0.8116 (ppp) cc_final: 0.7588 (mpp) REVERT: P 46 GLU cc_start: 0.4318 (mm-30) cc_final: 0.4106 (pp20) REVERT: P 72 ARG cc_start: 0.3514 (mtp85) cc_final: 0.2979 (ptp-170) REVERT: P 98 LYS cc_start: 0.4006 (ptmt) cc_final: 0.3318 (mmmt) REVERT: P 102 MET cc_start: 0.6783 (ppp) cc_final: 0.5227 (mpp) REVERT: X 31 HIS cc_start: 0.6427 (t70) cc_final: 0.6196 (t70) REVERT: X 101 PHE cc_start: 0.7197 (m-10) cc_final: 0.6895 (m-10) REVERT: Y 31 ASP cc_start: 0.8825 (m-30) cc_final: 0.8561 (t70) REVERT: Y 227 LYS cc_start: 0.3245 (tmtt) cc_final: 0.2855 (ttmt) outliers start: 32 outliers final: 21 residues processed: 257 average time/residue: 0.4602 time to fit residues: 196.5799 Evaluate side-chains 225 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain Y residue 102 MET Chi-restraints excluded: chain Y residue 117 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 390 optimal weight: 0.0470 chunk 421 optimal weight: 50.0000 chunk 347 optimal weight: 6.9990 chunk 387 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN A 658 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 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** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN P 54 ASN Y 3 GLN ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34641 Z= 0.220 Angle : 0.612 10.690 47148 Z= 0.307 Chirality : 0.047 0.285 5433 Planarity : 0.004 0.053 6072 Dihedral : 8.935 96.559 5196 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.44 % Allowed : 10.49 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.16 (0.13), residues: 4266 helix: 1.30 (0.20), residues: 662 sheet: -0.34 (0.15), residues: 1215 loop : -1.65 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 53 HIS 0.005 0.001 HIS C1048 PHE 0.032 0.001 PHE B 168 TYR 0.026 0.001 TYR O 54 ARG 0.005 0.000 ARG P 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7211 (m-80) cc_final: 0.6989 (m-10) REVERT: B 244 LEU cc_start: 0.5894 (tp) cc_final: 0.5671 (pt) REVERT: B 823 PHE cc_start: 0.7588 (m-80) cc_final: 0.7352 (m-80) REVERT: B 902 MET cc_start: 0.8395 (tpt) cc_final: 0.8140 (tpp) REVERT: A 237 ARG cc_start: 0.7740 (ptm-80) cc_final: 0.7306 (mtm110) REVERT: A 399 SER cc_start: 0.6593 (m) cc_final: 0.6321 (m) REVERT: A 400 PHE cc_start: 0.7550 (p90) cc_final: 0.7041 (p90) REVERT: A 1142 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7513 (tt0) REVERT: C 287 ASP cc_start: 0.7895 (t0) cc_final: 0.7321 (m-30) REVERT: C 740 MET cc_start: 0.8555 (tpt) cc_final: 0.8049 (mtt) REVERT: C 945 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7681 (pt) REVERT: C 1031 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: C 1114 ILE cc_start: 0.8771 (tp) cc_final: 0.8552 (mt) REVERT: C 1145 LEU cc_start: 0.7467 (mm) cc_final: 0.7192 (mm) REVERT: L 123 PHE cc_start: 0.4805 (m-80) cc_final: 0.4557 (m-80) REVERT: L 178 TYR cc_start: 0.5455 (m-10) cc_final: 0.4858 (m-10) REVERT: H 60 TYR cc_start: 0.6022 (m-80) cc_final: 0.5584 (m-80) REVERT: O 94 MET cc_start: 0.3210 (tmm) cc_final: 0.2925 (tmm) REVERT: P 46 GLU cc_start: 0.4493 (mm-30) cc_final: 0.4271 (pp20) REVERT: P 65 LYS cc_start: 0.3025 (tttt) cc_final: 0.1850 (mttt) REVERT: P 98 LYS cc_start: 0.4383 (ptmt) cc_final: 0.3684 (mmmt) REVERT: P 102 MET cc_start: 0.6892 (ppp) cc_final: 0.5295 (mpp) REVERT: X 31 HIS cc_start: 0.6359 (t70) cc_final: 0.6121 (t70) REVERT: X 101 PHE cc_start: 0.7219 (m-10) cc_final: 0.6958 (m-10) REVERT: Y 31 ASP cc_start: 0.8920 (m-30) cc_final: 0.8462 (p0) REVERT: Y 134 LYS cc_start: 0.4248 (tptp) cc_final: 0.3864 (mttt) REVERT: Y 227 LYS cc_start: 0.3487 (tmtt) cc_final: 0.3021 (ttmt) outliers start: 54 outliers final: 33 residues processed: 269 average time/residue: 0.4422 time to fit residues: 199.0745 Evaluate side-chains 235 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain Y residue 102 MET Chi-restraints excluded: chain Y residue 117 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 50.0000 chunk 293 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 391 optimal weight: 20.0000 chunk 414 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS H 77 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 34641 Z= 0.396 Angle : 0.688 11.942 47148 Z= 0.349 Chirality : 0.049 0.275 5433 Planarity : 0.005 0.054 6072 Dihedral : 8.219 94.707 5196 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.74 % Allowed : 11.98 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.29 (0.13), residues: 4266 helix: 1.04 (0.20), residues: 666 sheet: -0.40 (0.15), residues: 1233 loop : -1.72 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 40 HIS 0.008 0.001 HIS B1058 PHE 0.028 0.002 PHE A1121 TYR 0.023 0.002 TYR A1067 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 215 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.6000 (tp) cc_final: 0.5752 (pt) REVERT: B 696 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8819 (p) REVERT: B 902 MET cc_start: 0.8503 (tpt) cc_final: 0.8219 (tpp) REVERT: A 237 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7471 (mtp-110) REVERT: A 399 SER cc_start: 0.6627 (m) cc_final: 0.6358 (m) REVERT: A 400 PHE cc_start: 0.7573 (p90) cc_final: 0.7132 (p90) REVERT: A 819 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: A 1142 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7606 (tt0) REVERT: C 56 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7525 (tp) REVERT: C 287 ASP cc_start: 0.7982 (t0) cc_final: 0.7450 (m-30) REVERT: C 740 MET cc_start: 0.8562 (tpt) cc_final: 0.8091 (mtt) REVERT: C 945 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7915 (pp) REVERT: C 1031 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: C 1061 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8679 (m) REVERT: C 1114 ILE cc_start: 0.8840 (tp) cc_final: 0.8601 (mt) REVERT: L 40 TRP cc_start: 0.7760 (m100) cc_final: 0.6572 (m-10) REVERT: L 123 PHE cc_start: 0.4932 (m-80) cc_final: 0.4727 (m-80) REVERT: H 60 TYR cc_start: 0.5993 (m-80) cc_final: 0.5535 (m-80) REVERT: H 117 MET cc_start: 0.3602 (OUTLIER) cc_final: 0.2383 (mmm) REVERT: O 51 LEU cc_start: 0.2094 (OUTLIER) cc_final: 0.0975 (tt) REVERT: O 92 TYR cc_start: 0.3499 (OUTLIER) cc_final: 0.2912 (t80) REVERT: O 94 MET cc_start: 0.3283 (tmm) cc_final: 0.2991 (tmm) REVERT: P 46 GLU cc_start: 0.4558 (mm-30) cc_final: 0.4343 (pp20) REVERT: P 98 LYS cc_start: 0.4333 (ptmt) cc_final: 0.3719 (mmmt) REVERT: P 102 MET cc_start: 0.7003 (ppp) cc_final: 0.5440 (mpp) REVERT: X 101 PHE cc_start: 0.7181 (m-10) cc_final: 0.6885 (m-10) REVERT: Y 31 ASP cc_start: 0.8889 (m-30) cc_final: 0.8364 (p0) REVERT: Y 227 LYS cc_start: 0.3649 (tmtt) cc_final: 0.2899 (mttp) outliers start: 103 outliers final: 63 residues processed: 305 average time/residue: 0.4635 time to fit residues: 239.0320 Evaluate side-chains 274 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 202 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 112 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 30.0000 chunk 235 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 308 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 353 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN H 82 HIS ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 34641 Z= 0.354 Angle : 0.656 12.738 47148 Z= 0.333 Chirality : 0.048 0.312 5433 Planarity : 0.004 0.055 6072 Dihedral : 7.625 91.967 5196 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.27 % Allowed : 12.86 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.26 (0.13), residues: 4266 helix: 1.08 (0.20), residues: 665 sheet: -0.44 (0.15), residues: 1221 loop : -1.67 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 40 HIS 0.006 0.001 HIS B1058 PHE 0.025 0.002 PHE B1121 TYR 0.022 0.002 TYR A1067 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 220 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.8473 (tpt) cc_final: 0.8226 (tpp) REVERT: A 237 ARG cc_start: 0.7736 (ptm-80) cc_final: 0.7462 (mtp-110) REVERT: A 301 CYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6894 (m) REVERT: A 399 SER cc_start: 0.6573 (m) cc_final: 0.6336 (m) REVERT: A 400 PHE cc_start: 0.7561 (p90) cc_final: 0.7250 (p90) REVERT: A 819 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: A 996 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 1142 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7659 (tt0) REVERT: C 56 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7592 (tp) REVERT: C 287 ASP cc_start: 0.7981 (t0) cc_final: 0.7449 (m-30) REVERT: C 740 MET cc_start: 0.8566 (tpt) cc_final: 0.8107 (mtt) REVERT: C 1031 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: C 1061 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8670 (m) REVERT: C 1114 ILE cc_start: 0.8838 (tp) cc_final: 0.8609 (mt) REVERT: C 1145 LEU cc_start: 0.7292 (mm) cc_final: 0.6981 (mm) REVERT: L 121 PHE cc_start: 0.5283 (m-80) cc_final: 0.4710 (t80) REVERT: L 144 PHE cc_start: 0.3991 (p90) cc_final: 0.3618 (p90) REVERT: L 178 TYR cc_start: 0.5652 (m-10) cc_final: 0.4803 (m-10) REVERT: H 32 TYR cc_start: 0.6803 (m-10) cc_final: 0.6294 (m-10) REVERT: H 60 TYR cc_start: 0.6093 (m-80) cc_final: 0.5601 (m-80) REVERT: H 117 MET cc_start: 0.3532 (OUTLIER) cc_final: 0.2351 (mmm) REVERT: O 51 LEU cc_start: 0.2109 (OUTLIER) cc_final: 0.1399 (tt) REVERT: O 92 TYR cc_start: 0.3615 (OUTLIER) cc_final: 0.2991 (t80) REVERT: O 94 MET cc_start: 0.3215 (tmm) cc_final: 0.2993 (tmm) REVERT: P 98 LYS cc_start: 0.4368 (ptmt) cc_final: 0.3824 (mmtt) REVERT: P 102 MET cc_start: 0.6792 (ppp) cc_final: 0.5511 (mpp) REVERT: X 31 HIS cc_start: 0.6061 (t70) cc_final: 0.5783 (t70) REVERT: X 101 PHE cc_start: 0.7144 (m-10) cc_final: 0.6851 (m-10) REVERT: Y 31 ASP cc_start: 0.8863 (m-30) cc_final: 0.8296 (p0) REVERT: Y 227 LYS cc_start: 0.3643 (tmtt) cc_final: 0.2908 (mttp) outliers start: 123 outliers final: 82 residues processed: 331 average time/residue: 0.4262 time to fit residues: 240.1783 Evaluate side-chains 293 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 202 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain P residue 74 ASN Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 20.0000 chunk 373 optimal weight: 40.0000 chunk 81 optimal weight: 0.6980 chunk 243 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 chunk 415 optimal weight: 30.0000 chunk 344 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 1 GLN Y 3 GLN ** Y 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.157 34641 Z= 0.450 Angle : 0.713 12.755 47148 Z= 0.363 Chirality : 0.050 0.294 5433 Planarity : 0.005 0.057 6072 Dihedral : 7.714 91.708 5196 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.51 % Allowed : 14.03 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 4266 helix: 0.81 (0.19), residues: 672 sheet: -0.47 (0.15), residues: 1240 loop : -1.75 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 353 HIS 0.006 0.001 HIS A1058 PHE 0.030 0.002 PHE A1121 TYR 0.025 0.002 TYR A1067 ARG 0.004 0.000 ARG P 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 210 time to evaluate : 4.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 696 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8825 (t) REVERT: B 823 PHE cc_start: 0.7713 (m-80) cc_final: 0.7395 (m-80) REVERT: B 902 MET cc_start: 0.8488 (tpt) cc_final: 0.8259 (tpp) REVERT: A 237 ARG cc_start: 0.7709 (ptm-80) cc_final: 0.7439 (mtp-110) REVERT: A 301 CYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6907 (m) REVERT: A 996 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 1142 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7686 (tt0) REVERT: C 56 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7483 (tp) REVERT: C 287 ASP cc_start: 0.8005 (t0) cc_final: 0.7398 (m-30) REVERT: C 740 MET cc_start: 0.8579 (tpt) cc_final: 0.8219 (mtm) REVERT: C 1031 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: C 1061 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8687 (m) REVERT: C 1114 ILE cc_start: 0.8850 (tp) cc_final: 0.8616 (mt) REVERT: L 40 TRP cc_start: 0.7694 (m100) cc_final: 0.6677 (m100) REVERT: L 121 PHE cc_start: 0.5328 (m-80) cc_final: 0.4721 (t80) REVERT: L 144 PHE cc_start: 0.3810 (p90) cc_final: 0.3383 (p90) REVERT: L 178 TYR cc_start: 0.5661 (m-10) cc_final: 0.4835 (m-10) REVERT: H 32 TYR cc_start: 0.6852 (m-10) cc_final: 0.6307 (m-10) REVERT: H 60 TYR cc_start: 0.6052 (m-80) cc_final: 0.5552 (m-80) REVERT: H 117 MET cc_start: 0.3488 (OUTLIER) cc_final: 0.2249 (mmm) REVERT: O 92 TYR cc_start: 0.3476 (OUTLIER) cc_final: 0.2665 (t80) REVERT: O 94 MET cc_start: 0.2896 (tmm) cc_final: 0.2672 (tmm) REVERT: P 39 GLN cc_start: 0.6787 (tm-30) cc_final: 0.6457 (tm-30) REVERT: P 98 LYS cc_start: 0.4536 (ptmt) cc_final: 0.3653 (mtmm) REVERT: P 102 MET cc_start: 0.6795 (ppp) cc_final: 0.5565 (mpp) REVERT: X 31 HIS cc_start: 0.6135 (t70) cc_final: 0.5829 (t70) REVERT: X 101 PHE cc_start: 0.7212 (m-10) cc_final: 0.6879 (m-10) REVERT: Y 31 ASP cc_start: 0.8854 (m-30) cc_final: 0.8135 (p0) REVERT: Y 227 LYS cc_start: 0.3663 (tmtt) cc_final: 0.2936 (mttp) outliers start: 132 outliers final: 96 residues processed: 332 average time/residue: 0.4285 time to fit residues: 242.9507 Evaluate side-chains 304 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 200 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain P residue 74 ASN Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 349 optimal weight: 0.0770 chunk 231 optimal weight: 7.9990 chunk 413 optimal weight: 30.0000 chunk 258 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 overall best weight: 1.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 3 GLN Y 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34641 Z= 0.200 Angle : 0.592 13.161 47148 Z= 0.298 Chirality : 0.045 0.301 5433 Planarity : 0.004 0.054 6072 Dihedral : 6.899 85.525 5196 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.21 % Allowed : 15.36 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.03 (0.13), residues: 4266 helix: 1.50 (0.20), residues: 662 sheet: -0.32 (0.15), residues: 1207 loop : -1.56 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 53 HIS 0.004 0.001 HIS C1048 PHE 0.016 0.001 PHE A 92 TYR 0.019 0.001 TYR O 54 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 227 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.8404 (tpt) cc_final: 0.8120 (tpp) REVERT: A 237 ARG cc_start: 0.7712 (ptm-80) cc_final: 0.7289 (mtm110) REVERT: A 301 CYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6898 (m) REVERT: A 306 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 426 PRO cc_start: 0.6538 (Cg_exo) cc_final: 0.6185 (Cg_endo) REVERT: A 983 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7479 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7551 (tt0) REVERT: C 287 ASP cc_start: 0.7863 (t0) cc_final: 0.7377 (m-30) REVERT: C 740 MET cc_start: 0.8557 (tpt) cc_final: 0.8090 (mtt) REVERT: C 1031 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: C 1061 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8655 (m) REVERT: C 1114 ILE cc_start: 0.8805 (tp) cc_final: 0.8603 (mt) REVERT: C 1145 LEU cc_start: 0.7286 (mm) cc_final: 0.6909 (mm) REVERT: L 121 PHE cc_start: 0.5311 (m-80) cc_final: 0.4787 (t80) REVERT: L 144 PHE cc_start: 0.3859 (p90) cc_final: 0.3516 (p90) REVERT: L 178 TYR cc_start: 0.5248 (m-10) cc_final: 0.4424 (m-10) REVERT: H 32 TYR cc_start: 0.6668 (m-10) cc_final: 0.6113 (m-10) REVERT: H 60 TYR cc_start: 0.6033 (m-80) cc_final: 0.5479 (m-80) REVERT: H 117 MET cc_start: 0.3566 (OUTLIER) cc_final: 0.2457 (mmm) REVERT: O 92 TYR cc_start: 0.3785 (OUTLIER) cc_final: 0.2957 (t80) REVERT: O 94 MET cc_start: 0.2624 (tmm) cc_final: 0.2419 (tmm) REVERT: P 98 LYS cc_start: 0.4159 (ptmt) cc_final: 0.3609 (mmtp) REVERT: P 102 MET cc_start: 0.6799 (ppp) cc_final: 0.5530 (mpp) REVERT: X 31 HIS cc_start: 0.6239 (t70) cc_final: 0.5681 (t-90) REVERT: X 101 PHE cc_start: 0.7158 (m-10) cc_final: 0.6834 (m-10) REVERT: Y 31 ASP cc_start: 0.8804 (m-30) cc_final: 0.8112 (p0) REVERT: Y 227 LYS cc_start: 0.3515 (tmtt) cc_final: 0.2912 (mttp) outliers start: 83 outliers final: 63 residues processed: 302 average time/residue: 0.4374 time to fit residues: 224.7129 Evaluate side-chains 274 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 205 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 124 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 262 optimal weight: 0.0870 chunk 281 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 325 optimal weight: 10.0000 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34641 Z= 0.167 Angle : 0.570 13.490 47148 Z= 0.286 Chirality : 0.045 0.283 5433 Planarity : 0.004 0.050 6072 Dihedral : 6.459 81.867 5196 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.08 % Allowed : 16.11 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -0.84 (0.13), residues: 4266 helix: 1.70 (0.20), residues: 663 sheet: -0.27 (0.15), residues: 1231 loop : -1.42 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 PHE 0.016 0.001 PHE C 238 TYR 0.017 0.001 TYR O 54 ARG 0.003 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 232 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 823 PHE cc_start: 0.7701 (m-80) cc_final: 0.7463 (m-80) REVERT: B 902 MET cc_start: 0.8393 (tpt) cc_final: 0.8163 (tpp) REVERT: A 168 PHE cc_start: 0.7830 (t80) cc_final: 0.7472 (t80) REVERT: A 301 CYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6873 (m) REVERT: A 983 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7639 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7609 (tt0) REVERT: C 287 ASP cc_start: 0.7802 (t0) cc_final: 0.7361 (m-30) REVERT: C 740 MET cc_start: 0.8542 (tpt) cc_final: 0.8171 (mtt) REVERT: C 1031 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 1061 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8592 (m) REVERT: C 1144 GLU cc_start: 0.7747 (mp0) cc_final: 0.7487 (mp0) REVERT: C 1145 LEU cc_start: 0.7235 (mm) cc_final: 0.6877 (mm) REVERT: L 4 MET cc_start: 0.5288 (ptm) cc_final: 0.4984 (ttp) REVERT: L 121 PHE cc_start: 0.5311 (m-80) cc_final: 0.4826 (t80) REVERT: L 144 PHE cc_start: 0.3867 (p90) cc_final: 0.3516 (p90) REVERT: L 178 TYR cc_start: 0.5220 (m-10) cc_final: 0.4388 (m-10) REVERT: H 60 TYR cc_start: 0.6010 (m-80) cc_final: 0.5452 (m-80) REVERT: H 117 MET cc_start: 0.4026 (OUTLIER) cc_final: 0.2999 (mmm) REVERT: O 92 TYR cc_start: 0.3742 (OUTLIER) cc_final: 0.2914 (t80) REVERT: P 98 LYS cc_start: 0.4075 (ptmt) cc_final: 0.3533 (mmtp) REVERT: P 102 MET cc_start: 0.7009 (ppp) cc_final: 0.5792 (mpp) REVERT: X 31 HIS cc_start: 0.6240 (t70) cc_final: 0.5884 (t70) REVERT: X 101 PHE cc_start: 0.7165 (m-10) cc_final: 0.6923 (m-10) REVERT: Y 31 ASP cc_start: 0.8795 (m-30) cc_final: 0.8110 (p0) REVERT: Y 227 LYS cc_start: 0.3455 (tmtt) cc_final: 0.2831 (mttp) outliers start: 78 outliers final: 63 residues processed: 302 average time/residue: 0.4431 time to fit residues: 227.0554 Evaluate side-chains 273 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 205 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 112 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 50.0000 chunk 396 optimal weight: 7.9990 chunk 361 optimal weight: 40.0000 chunk 385 optimal weight: 0.0270 chunk 231 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 348 optimal weight: 0.2980 chunk 364 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 overall best weight: 2.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 1 GLN Y 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 34641 Z= 0.320 Angle : 0.640 13.276 47148 Z= 0.324 Chirality : 0.047 0.319 5433 Planarity : 0.004 0.050 6072 Dihedral : 6.693 81.824 5196 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.61 % Allowed : 15.95 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -0.99 (0.13), residues: 4266 helix: 1.40 (0.20), residues: 664 sheet: -0.23 (0.15), residues: 1221 loop : -1.54 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 40 HIS 0.005 0.001 HIS B1058 PHE 0.023 0.002 PHE A1121 TYR 0.021 0.001 TYR A1067 ARG 0.007 0.000 ARG P 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 214 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.5992 (p) REVERT: B 902 MET cc_start: 0.8497 (tpt) cc_final: 0.8226 (tpp) REVERT: A 168 PHE cc_start: 0.7853 (t80) cc_final: 0.7634 (t80) REVERT: A 301 CYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6907 (m) REVERT: A 306 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8153 (t80) REVERT: A 426 PRO cc_start: 0.6623 (Cg_exo) cc_final: 0.6291 (Cg_endo) REVERT: A 819 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: A 983 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7559 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7668 (tt0) REVERT: C 56 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7668 (tt) REVERT: C 287 ASP cc_start: 0.7861 (t0) cc_final: 0.7371 (m-30) REVERT: C 740 MET cc_start: 0.8574 (tpt) cc_final: 0.8203 (mtm) REVERT: C 1031 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: C 1061 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8647 (m) REVERT: C 1144 GLU cc_start: 0.7720 (mp0) cc_final: 0.7458 (mp0) REVERT: C 1145 LEU cc_start: 0.7174 (mm) cc_final: 0.6801 (mm) REVERT: L 121 PHE cc_start: 0.5432 (m-80) cc_final: 0.4914 (t80) REVERT: L 144 PHE cc_start: 0.3854 (p90) cc_final: 0.3492 (p90) REVERT: L 178 TYR cc_start: 0.5436 (m-10) cc_final: 0.4635 (m-10) REVERT: H 117 MET cc_start: 0.3698 (OUTLIER) cc_final: 0.2627 (mmm) REVERT: H 134 LYS cc_start: 0.5640 (mtpp) cc_final: 0.5421 (ttpp) REVERT: O 92 TYR cc_start: 0.3663 (OUTLIER) cc_final: 0.2871 (t80) REVERT: P 98 LYS cc_start: 0.4063 (ptmt) cc_final: 0.3483 (mmtp) REVERT: P 102 MET cc_start: 0.7077 (ppp) cc_final: 0.5896 (mpp) REVERT: X 31 HIS cc_start: 0.6281 (t70) cc_final: 0.5928 (t70) REVERT: X 101 PHE cc_start: 0.7160 (m-10) cc_final: 0.6875 (m-10) REVERT: Y 31 ASP cc_start: 0.8798 (m-30) cc_final: 0.8111 (p0) REVERT: Y 227 LYS cc_start: 0.3418 (tmtt) cc_final: 0.2843 (mttp) outliers start: 98 outliers final: 75 residues processed: 304 average time/residue: 0.4253 time to fit residues: 219.2462 Evaluate side-chains 287 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 203 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 112 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 0.9990 chunk 407 optimal weight: 40.0000 chunk 248 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 283 optimal weight: 0.4980 chunk 427 optimal weight: 20.0000 chunk 393 optimal weight: 0.9980 chunk 340 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 262 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 209 GLN ** Y 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34641 Z= 0.177 Angle : 0.574 13.332 47148 Z= 0.288 Chirality : 0.045 0.291 5433 Planarity : 0.004 0.050 6072 Dihedral : 6.278 78.840 5196 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.08 % Allowed : 16.64 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4266 helix: 1.76 (0.20), residues: 663 sheet: -0.16 (0.15), residues: 1227 loop : -1.42 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 40 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE A 92 TYR 0.016 0.001 TYR O 54 ARG 0.004 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8532 Ramachandran restraints generated. 4266 Oldfield, 0 Emsley, 4266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 218 time to evaluate : 3.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.6136 (OUTLIER) cc_final: 0.5648 (p) REVERT: B 902 MET cc_start: 0.8391 (tpt) cc_final: 0.8172 (tpp) REVERT: A 129 LYS cc_start: 0.7416 (tmtt) cc_final: 0.6985 (tmtt) REVERT: A 168 PHE cc_start: 0.7866 (t80) cc_final: 0.7590 (t80) REVERT: A 301 CYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6896 (m) REVERT: A 306 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8184 (t80) REVERT: A 983 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7617 (ptt-90) REVERT: A 1142 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7673 (tt0) REVERT: C 56 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7645 (tt) REVERT: C 287 ASP cc_start: 0.7834 (t0) cc_final: 0.7383 (m-30) REVERT: C 740 MET cc_start: 0.8518 (tpt) cc_final: 0.8085 (mtt) REVERT: C 1031 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: C 1061 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8599 (m) REVERT: C 1144 GLU cc_start: 0.7744 (mp0) cc_final: 0.7471 (mp0) REVERT: C 1145 LEU cc_start: 0.7178 (mm) cc_final: 0.6817 (mm) REVERT: L 94 MET cc_start: 0.5558 (mmm) cc_final: 0.5012 (mmm) REVERT: L 121 PHE cc_start: 0.5376 (m-80) cc_final: 0.4882 (t80) REVERT: L 144 PHE cc_start: 0.3844 (p90) cc_final: 0.3497 (p90) REVERT: L 178 TYR cc_start: 0.5407 (m-10) cc_final: 0.4654 (m-10) REVERT: H 60 TYR cc_start: 0.6299 (m-80) cc_final: 0.5628 (m-80) REVERT: H 102 MET cc_start: 0.7949 (ppp) cc_final: 0.7733 (ttm) REVERT: H 117 MET cc_start: 0.3306 (OUTLIER) cc_final: 0.2223 (mmm) REVERT: O 92 TYR cc_start: 0.3580 (OUTLIER) cc_final: 0.2826 (t80) REVERT: P 98 LYS cc_start: 0.4019 (ptmt) cc_final: 0.3329 (ptmt) REVERT: P 102 MET cc_start: 0.6854 (ppp) cc_final: 0.5902 (mpp) REVERT: X 31 HIS cc_start: 0.6337 (t70) cc_final: 0.5994 (t70) REVERT: X 101 PHE cc_start: 0.7191 (m-10) cc_final: 0.6966 (m-10) REVERT: Y 31 ASP cc_start: 0.8853 (m-30) cc_final: 0.8221 (p0) REVERT: Y 227 LYS cc_start: 0.3399 (tmtt) cc_final: 0.2817 (mttp) outliers start: 78 outliers final: 65 residues processed: 288 average time/residue: 0.4464 time to fit residues: 218.4526 Evaluate side-chains 277 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 204 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 TRP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 225 ASP Chi-restraints excluded: chain O residue 54 TYR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 112 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 7.9990 chunk 362 optimal weight: 8.9990 chunk 104 optimal weight: 0.0070 chunk 313 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 340 optimal weight: 40.0000 chunk 142 optimal weight: 9.9990 chunk 350 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 129 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 = 0.4425 r_free = 0.4425 target = 0.187263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.144465 restraints weight = 57192.605| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.34 r_work: 0.3323 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.154 34641 Z= 0.434 Angle : 0.700 13.653 47148 Z= 0.356 Chirality : 0.049 0.329 5433 Planarity : 0.005 0.053 6072 Dihedral : 6.849 89.899 5196 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.61 % Allowed : 16.45 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.33 % 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: -1.10 (0.13), residues: 4266 helix: 1.13 (0.20), residues: 667 sheet: -0.27 (0.15), residues: 1222 loop : -1.58 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 40 HIS 0.008 0.001 HIS B1058 PHE 0.032 0.002 PHE A1121 TYR 0.026 0.002 TYR A1067 ARG 0.008 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6745.94 seconds wall clock time: 124 minutes 48.04 seconds (7488.04 seconds total)