Starting phenix.real_space_refine on Sat Dec 16 01:57:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9n_31033/12_2023/7e9n_31033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9n_31033/12_2023/7e9n_31033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9n_31033/12_2023/7e9n_31033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9n_31033/12_2023/7e9n_31033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9n_31033/12_2023/7e9n_31033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9n_31033/12_2023/7e9n_31033.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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 145 5.16 5 C 21280 2.51 5 N 5554 2.21 5 O 6540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "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 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "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 ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 1144": "OE1" <-> "OE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 113": "NH1" <-> "NH2" Residue "O PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 148": "OE1" <-> "OE2" Residue "O ASP 172": "OD1" <-> "OD2" Residue "O ASP 175": "OD1" <-> "OD2" Residue "O ASP 190": "OD1" <-> "OD2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 73": "OD1" <-> "OD2" Residue "P TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P GLU 114": "OE1" <-> "OE2" Residue "P TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 118": "OD1" <-> "OD2" Residue "P PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 75": "OD1" <-> "OD2" Residue "X PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 82": "NH1" <-> "NH2" Residue "X GLU 84": "OE1" <-> "OE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "X ASP 190": "OD1" <-> "OD2" Residue "X GLU 192": "OE1" <-> "OE2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y ASP 73": "OD1" <-> "OD2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y GLU 114": "OE1" <-> "OE2" Residue "Y ASP 118": "OD1" <-> "OD2" Residue "Y PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 170": "OE1" <-> "OE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33519 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7805 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7535 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 52, 'TRANS': 924} Chain breaks: 11 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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': 1, 'PTRANS': 11, '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: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1655 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1653 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1664 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 17.48, per 1000 atoms: 0.52 Number of scatterers: 33519 At special positions: 0 Unit cell: (169.725, 196.005, 227.76, 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 145 16.00 O 6540 8.00 N 5554 7.00 C 21280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.02 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=2.04 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 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=2.03 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=2.03 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 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 331 " " 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 A1098 " " 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 C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 12.71 Conformation dependent library (CDL) restraints added in 6.4 seconds 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8026 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 67 sheets defined 18.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.245A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.537A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.910A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.377A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.557A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.568A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.554A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.812A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.284A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.230A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.925A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.604A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.460A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.623A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.642A 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 945 through 965 removed outlier: 4.148A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.646A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.325A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.760A pdb=" N GLY C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 408 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.731A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 4.319A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.873A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.548A 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: 3.595A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.734A 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 removed outlier: 3.504A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.633A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (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 982 removed outlier: 3.913A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.439A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.804A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 88 removed outlier: 3.749A 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 188 through 194 removed outlier: 3.650A pdb=" N GLU O 192 " --> pdb=" O LYS O 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS O 194 " --> pdb=" O ASP O 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.224A pdb=" N ASP P 31 " --> pdb=" O THR P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.506A pdb=" N VAL P 64 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS P 65 " --> pdb=" O ASP P 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 65' Processing helix chain 'P' and resid 173 through 175 No H-bonds generated for 'chain 'P' and resid 173 through 175' Processing helix chain 'X' and resid 84 through 88 removed outlier: 3.985A pdb=" N VAL X 88 " --> pdb=" O ALA X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 131 Processing helix chain 'X' and resid 188 through 194 removed outlier: 3.843A pdb=" N GLU X 192 " --> pdb=" O LYS X 188 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS X 194 " --> pdb=" O ASP X 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 removed outlier: 4.134A pdb=" N ASP Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 28 through 32' Processing helix chain 'Y' and resid 61 through 65 removed outlier: 4.043A pdb=" N LYS Y 65 " --> pdb=" O ASP Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 175 No H-bonds generated for 'chain 'Y' and resid 173 through 175' Processing helix chain 'Y' and resid 204 through 206 No H-bonds generated for 'chain 'Y' and resid 204 through 206' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.112A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.816A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.912A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.620A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.750A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 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 654 through 655 removed outlier: 6.541A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.051A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AB2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB3, first strand: chain 'B' and resid 1094 through 1098 removed outlier: 3.593A pdb=" N ASN B1098 " --> pdb=" O HIS B1101 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B1101 " --> pdb=" O ASN B1098 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.067A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.575A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.762A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.558A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.632A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.525A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.193A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.626A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC9, first strand: chain 'A' and resid 1094 through 1098 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.173A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.723A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.674A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.668A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.275A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.551A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.939A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.122A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'O' and resid 50 through 53 removed outlier: 6.487A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 119 through 123 Processing sheet with id=AE9, first strand: chain 'O' and resid 150 through 155 Processing sheet with id=AF1, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'P' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'P' and resid 46 through 51 removed outlier: 6.915A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET P 34 " --> pdb=" O GLY P 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 137 through 141 removed outlier: 6.444A pdb=" N TYR P 193 " --> pdb=" O ASP P 161 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N SER P 194 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA P 185 " --> pdb=" O SER P 194 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER P 196 " --> pdb=" O PHE P 183 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 168 through 171 Processing sheet with id=AF6, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'X' and resid 50 through 53 removed outlier: 6.446A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 119 through 123 Processing sheet with id=AF9, first strand: chain 'X' and resid 150 through 154 Processing sheet with id=AG1, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'Y' and resid 57 through 59 removed outlier: 7.034A pdb=" N GLY Y 50 " --> pdb=" O ILE Y 58 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 34 " --> pdb=" O GLY Y 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 137 through 141 removed outlier: 6.558A pdb=" N TYR Y 193 " --> pdb=" O ASP Y 161 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER Y 194 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA Y 185 " --> pdb=" O SER Y 194 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER Y 196 " --> pdb=" O PHE Y 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE Y 183 " --> pdb=" O SER Y 196 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 168 through 171 Processing sheet with id=AG6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.562A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.920A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.771A pdb=" N VAL L 155 " --> pdb=" O ALA L 158 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.666A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.009A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 167 through 171 1290 hydrogen bonds defined for protein. 3411 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: 14.83 Time building geometry restraints manager: 13.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5551 1.32 - 1.45: 10002 1.45 - 1.59: 18533 1.59 - 1.72: 0 1.72 - 1.86: 186 Bond restraints: 34272 Sorted by residual: bond pdb=" C7 NAG A1305 " pdb=" N2 NAG A1305 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C7 NAG A1306 " pdb=" N2 NAG A1306 " ideal model delta sigma weight residual 1.346 1.460 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C7 NAG A1309 " pdb=" N2 NAG A1309 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C7 NAG C1303 " pdb=" N2 NAG C1303 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 34267 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.20: 965 106.20 - 113.23: 18719 113.23 - 120.25: 12289 120.25 - 127.27: 14384 127.27 - 134.30: 312 Bond angle restraints: 46669 Sorted by residual: angle pdb=" N GLN C 913 " pdb=" CA GLN C 913 " pdb=" C GLN C 913 " ideal model delta sigma weight residual 112.89 121.03 -8.14 1.24e+00 6.50e-01 4.31e+01 angle pdb=" N GLN A 913 " pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 112.23 118.92 -6.69 1.26e+00 6.30e-01 2.82e+01 angle pdb=" CA GLY Y 116 " pdb=" C GLY Y 116 " pdb=" O GLY Y 116 " ideal model delta sigma weight residual 122.59 118.33 4.26 1.04e+00 9.25e-01 1.68e+01 angle pdb=" N GLU B 281 " pdb=" CA GLU B 281 " pdb=" C GLU B 281 " ideal model delta sigma weight residual 111.33 116.26 -4.93 1.21e+00 6.83e-01 1.66e+01 angle pdb=" N GLU A 406 " pdb=" CA GLU A 406 " pdb=" C GLU A 406 " ideal model delta sigma weight residual 113.15 108.49 4.66 1.19e+00 7.06e-01 1.53e+01 ... (remaining 46664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 19592 24.42 - 48.84: 1017 48.84 - 73.26: 119 73.26 - 97.68: 35 97.68 - 122.10: 20 Dihedral angle restraints: 20783 sinusoidal: 8302 harmonic: 12481 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 2.74 -88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.82 -86.82 1 1.00e+01 1.00e-02 9.07e+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 93.00 177.87 -84.87 1 1.00e+01 1.00e-02 8.74e+01 ... (remaining 20780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4979 0.104 - 0.208: 404 0.208 - 0.313: 14 0.313 - 0.417: 1 0.417 - 0.521: 2 Chirality restraints: 5400 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.17e+00 ... (remaining 5397 not shown) Planarity restraints: 6038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " -0.064 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO C 225 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Y 163 " 0.061 5.00e-02 4.00e+02 9.08e-02 1.32e+01 pdb=" N PRO Y 164 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO Y 164 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO Y 164 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 84 " -0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO B 85 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " -0.046 5.00e-02 4.00e+02 ... (remaining 6035 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4874 2.75 - 3.29: 32435 3.29 - 3.83: 52034 3.83 - 4.36: 60246 4.36 - 4.90: 106050 Nonbonded interactions: 255639 Sorted by model distance: nonbonded pdb=" O GLY C1085 " pdb=" N CYS C1126 " model vdw 2.217 2.520 nonbonded pdb=" O PHE C 106 " pdb=" OG SER C 116 " model vdw 2.223 2.440 nonbonded pdb=" O ASN B 422 " pdb=" NH2 ARG B 454 " model vdw 2.224 2.520 nonbonded pdb=" NH1 ARG B 34 " pdb=" OE2 GLU B 191 " model vdw 2.231 2.520 nonbonded pdb=" O GLN Y 39 " pdb=" N LEU Y 93 " model vdw 2.231 2.520 ... (remaining 255634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 213 or (resid 214 and (name N or name CA or nam \ e C or name O or name CB )) or resid 215 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 377 or (resid 3 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 379 through \ 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) or r \ esid 529 through 723 or (resid 724 and (name N or name CA or name C or name O or \ name CB )) or resid 725 through 813 or (resid 814 and (name N or name CA or nam \ e C or name O or name CB )) or resid 815 through 1147 or resid 1301 through 1309 \ )) selection = (chain 'B' and (resid 27 through 331 or (resid 332 through 333 and (name N or na \ me CA or name C or name O or name CB )) or resid 334 through 368 or (resid 369 a \ nd (name N or name CA or name C or name O or name CB )) or resid 370 through 402 \ or (resid 403 and (name N or name CA or name C or name O or name CB )) or resid \ 404 or (resid 405 through 408 and (name N or name CA or name C or name O or nam \ e CB )) or resid 409 through 413 or (resid 414 through 415 and (name N or name C \ A or name C or name O or name CB )) or resid 416 or (resid 417 and (name N or na \ me CA or name C or name O or name CB )) or resid 418 through 419 or (resid 420 a \ nd (name N or name CA or name C or name O or name CB )) or resid 421 through 423 \ or (resid 424 and (name N or name CA or name C or name O or name CB )) or resid \ 425 through 440 or (resid 441 and (name N or name CA or name C or name O or nam \ e CB )) or resid 442 through 443 or (resid 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or (resid 460 and (name N or name CA or \ name C or name O or name CB )) or resid 461 through 464 or (resid 465 and (name \ N or name CA or name C or name O or name CB )) or resid 466 or (resid 467 throug \ h 469 and (name N or name CA or name C or name O or name CB )) or resid 470 or ( \ resid 471 through 473 and (name N or name CA or name C or name O or name CB )) o \ r resid 487 through 497 or (resid 498 and (name N or name CA or name C or name O \ or name CB )) or resid 499 through 500 or resid 503 through 504 or (resid 505 a \ nd (name N or name CA or name C or name O or name CB )) or resid 506 through 515 \ or (resid 516 and (name N or name CA or name C or name O or name CB )) or resid \ 517 through 518 or (resid 519 through 520 and (name N or name CA or name C or n \ ame O or name CB )) or resid 521 through 723 or (resid 724 and (name N or name C \ A or name C or name O or name CB )) or resid 725 through 1147 or resid 1301 thro \ ugh 1309)) selection = (chain 'C' and (resid 27 through 213 or (resid 214 and (name N or name CA or nam \ e C or name O or name CB )) or resid 215 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 331 or (resid 3 \ 32 through 333 and (name N or name CA or name C or name O or name CB )) or resid \ 334 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 through 377 or (resid 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 402 or (resid 403 and (name N or na \ me CA or name C or name O or name CB )) or resid 404 or (resid 405 through 408 a \ nd (name N or name CA or name C or name O or name CB )) or resid 409 through 413 \ or (resid 414 through 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or nam \ e CB )) or resid 418 through 419 or (resid 420 and (name N or name CA or name C \ or name O or name CB )) or resid 421 through 423 or (resid 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 through 440 or (resid 441 a \ nd (name N or name CA or name C or name O or name CB )) or resid 442 through 443 \ or (resid 449 and (name N or name CA or name C or name O or name CB )) or resid \ 450 through 453 or (resid 454 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 460 and (name N or name CA or name C or name O or name CB )) o \ r resid 461 through 464 or (resid 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 or (resid 467 through 469 and (name N or name CA or \ name C or name O or name CB )) or resid 470 or (resid 471 through 473 and (name \ N or name CA or name C or name O or name CB )) or resid 487 through 497 or (resi \ d 498 and (name N or name CA or name C or name O or name CB )) or resid 499 thro \ ugh 500 or resid 503 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 515 or (resid 516 and (name N or na \ me CA or name C or name O or name CB )) or resid 517 through 518 or (resid 519 t \ hrough 520 and (name N or name CA or name C or name O or name CB )) or resid 521 \ through 527 or (resid 528 and (name N or name CA or name C or name O or name CB \ )) or resid 529 through 813 or (resid 814 and (name N or name CA or name C or n \ ame O or name CB )) or resid 815 through 1147 or resid 1301 through 1309)) } ncs_group { reference = (chain 'H' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 116 or (resid 117 and (name N or \ name CA or name C or name O or name CB )) or resid 118 through 198 or (resid 199 \ and (name N or name CA or name C or name O or name CB )) or resid 200 through 2 \ 32)) selection = (chain 'P' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 116 or (resid 117 and (name N or \ name CA or name C or name O or name CB )) or resid 118 through 198 or (resid 199 \ and (name N or name CA or name C or name O or name CB )) or resid 200 through 2 \ 08 or (resid 209 and (name N or name CA or name C or name O or name CB )) or res \ id 210 through 232)) selection = (chain 'Y' and (resid 1 through 208 or (resid 209 and (name N or name CA or name \ C or name O or name CB )) or resid 210 through 232)) } ncs_group { reference = (chain 'L' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 146 or (resid 147 a \ nd (name N or name CA or name C or name O or name CB )) or resid 148 through 192 \ or (resid 193 and (name N or name CA or name C or name O or name CB )) or resid \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 218)) selection = (chain 'O' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 78 or (resid 79 and (name N or name \ CA or name C or name O or name CB )) or resid 80 through 146 or (resid 147 and \ (name N or name CA or name C or name O or name CB )) or resid 148 through 192 or \ (resid 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 4 or (resid 195 and (name N or name CA or name C or name O or name CB )) or resi \ d 196 through 218)) selection = (chain 'X' and (resid 1 through 78 or (resid 79 and (name N or name CA or name C \ or name O or name CB )) or resid 80 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 218)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 9.580 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 88.350 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.009 0.116 34272 Z= 0.607 Angle : 0.921 10.365 46669 Z= 0.518 Chirality : 0.058 0.521 5400 Planarity : 0.006 0.100 6011 Dihedral : 14.954 122.100 12613 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.05 % Allowed : 1.06 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -2.35 (0.12), residues: 4233 helix: -0.15 (0.20), residues: 641 sheet: -1.09 (0.14), residues: 1287 loop : -2.32 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Y 171 HIS 0.023 0.002 HIS C1064 PHE 0.055 0.003 PHE B 906 TYR 0.046 0.002 TYR A 904 ARG 0.012 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.5226 time to fit residues: 169.5119 Evaluate side-chains 94 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 3.689 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 129 optimal weight: 0.4980 chunk 203 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 386 optimal weight: 50.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 370 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1048 HIS B1113 GLN A 343 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 965 GLN C 360 ASN C 751 ASN C 804 GLN C 901 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 HIS ** O 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 ASN ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 215 ASN Y 1 GLN Y 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34272 Z= 0.219 Angle : 0.606 8.518 46669 Z= 0.311 Chirality : 0.045 0.355 5400 Planarity : 0.005 0.065 6011 Dihedral : 8.928 114.178 5156 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.65 % Allowed : 7.34 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.72 (0.13), residues: 4233 helix: 1.09 (0.21), residues: 657 sheet: -0.87 (0.14), residues: 1312 loop : -2.04 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 36 HIS 0.008 0.001 HIS X 203 PHE 0.026 0.001 PHE X 144 TYR 0.019 0.001 TYR C 904 ARG 0.009 0.001 ARG O 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 4.150 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 outliers start: 24 outliers final: 14 residues processed: 125 average time/residue: 0.5179 time to fit residues: 106.0565 Evaluate side-chains 101 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3146 time to fit residues: 13.2867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 387 optimal weight: 20.0000 chunk 418 optimal weight: 7.9990 chunk 345 optimal weight: 4.9990 chunk 384 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 310 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1010 GLN A1106 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 487 ASN P 3 GLN ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34272 Z= 0.344 Angle : 0.642 8.610 46669 Z= 0.332 Chirality : 0.046 0.382 5400 Planarity : 0.005 0.058 6011 Dihedral : 8.124 118.702 5156 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.60 % Allowed : 11.83 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.60 (0.13), residues: 4233 helix: 1.14 (0.20), residues: 655 sheet: -0.74 (0.14), residues: 1314 loop : -1.98 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 171 HIS 0.005 0.001 HIS B1064 PHE 0.021 0.002 PHE X 76 TYR 0.017 0.002 TYR A 204 ARG 0.006 0.001 ARG O 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 120 average time/residue: 0.4988 time to fit residues: 99.5275 Evaluate side-chains 94 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3131 time to fit residues: 9.6493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 0.9980 chunk 291 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 42 optimal weight: 40.0000 chunk 184 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 388 optimal weight: 0.0050 chunk 411 optimal weight: 30.0000 chunk 203 optimal weight: 7.9990 chunk 368 optimal weight: 0.9990 chunk 110 optimal weight: 0.0770 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 804 GLN A 935 GLN A 965 GLN A1010 GLN A1106 GLN C1088 HIS C1101 HIS ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34272 Z= 0.132 Angle : 0.527 9.256 46669 Z= 0.269 Chirality : 0.043 0.299 5400 Planarity : 0.004 0.053 6011 Dihedral : 7.265 114.938 5156 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.06 % Allowed : 12.59 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: 4233 helix: 1.87 (0.21), residues: 651 sheet: -0.47 (0.14), residues: 1326 loop : -1.74 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.006 0.001 HIS B1048 PHE 0.022 0.001 PHE X 76 TYR 0.013 0.001 TYR B1067 ARG 0.018 0.000 ARG X 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 9 residues processed: 136 average time/residue: 0.4678 time to fit residues: 111.0668 Evaluate side-chains 94 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 3.865 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3472 time to fit residues: 10.7433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 40.0000 chunk 233 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 351 optimal weight: 30.0000 chunk 284 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 369 optimal weight: 7.9990 chunk 103 optimal weight: 0.0970 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 872 GLN A 935 GLN A 965 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 HIS ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN L 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 34272 Z= 0.345 Angle : 0.614 8.803 46669 Z= 0.318 Chirality : 0.046 0.510 5400 Planarity : 0.004 0.063 6011 Dihedral : 7.762 119.285 5156 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.22 % Allowed : 14.05 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.23 (0.13), residues: 4233 helix: 1.47 (0.21), residues: 649 sheet: -0.50 (0.14), residues: 1327 loop : -1.76 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 171 HIS 0.006 0.001 HIS H 35 PHE 0.020 0.002 PHE A 906 TYR 0.015 0.002 TYR B1067 ARG 0.003 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 90 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 16 residues processed: 130 average time/residue: 0.4403 time to fit residues: 99.6200 Evaluate side-chains 97 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 3.859 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3111 time to fit residues: 14.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 8.9990 chunk 370 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 101 optimal weight: 0.2980 chunk 412 optimal weight: 50.0000 chunk 342 optimal weight: 50.0000 chunk 190 optimal weight: 4.9990 chunk 34 optimal weight: 30.0000 chunk 136 optimal weight: 0.3980 chunk 216 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 901 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 142 ASN O 143 ASN ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34272 Z= 0.271 Angle : 0.574 11.622 46669 Z= 0.295 Chirality : 0.044 0.433 5400 Planarity : 0.004 0.070 6011 Dihedral : 7.505 118.137 5156 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.97 % Allowed : 14.60 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -1.14 (0.13), residues: 4233 helix: 1.61 (0.21), residues: 649 sheet: -0.47 (0.14), residues: 1318 loop : -1.68 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 171 HIS 0.006 0.001 HIS H 35 PHE 0.015 0.001 PHE A 906 TYR 0.015 0.001 TYR A 741 ARG 0.004 0.000 ARG X 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 85 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 118 average time/residue: 0.4345 time to fit residues: 91.3060 Evaluate side-chains 102 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 3.880 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3209 time to fit residues: 17.7320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 233 optimal weight: 0.8980 chunk 346 optimal weight: 30.0000 chunk 230 optimal weight: 0.5980 chunk 410 optimal weight: 50.0000 chunk 256 optimal weight: 0.7980 chunk 250 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN A 965 GLN A1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34272 Z= 0.136 Angle : 0.520 9.619 46669 Z= 0.264 Chirality : 0.043 0.313 5400 Planarity : 0.004 0.071 6011 Dihedral : 6.988 115.269 5156 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.51 % Allowed : 15.03 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.83 (0.13), residues: 4233 helix: 2.05 (0.21), residues: 650 sheet: -0.31 (0.14), residues: 1329 loop : -1.54 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS B1048 PHE 0.014 0.001 PHE C 456 TYR 0.013 0.001 TYR B1067 ARG 0.004 0.000 ARG X 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 108 average time/residue: 0.4856 time to fit residues: 90.2879 Evaluate side-chains 84 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 3.857 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3338 time to fit residues: 7.4779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 0.1980 chunk 163 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 279 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 322 optimal weight: 20.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1106 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34272 Z= 0.295 Angle : 0.584 10.134 46669 Z= 0.299 Chirality : 0.044 0.383 5400 Planarity : 0.004 0.071 6011 Dihedral : 7.348 118.495 5156 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.54 % Allowed : 15.54 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.95 (0.13), residues: 4233 helix: 1.78 (0.21), residues: 649 sheet: -0.37 (0.14), residues: 1347 loop : -1.57 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 PHE 0.016 0.001 PHE B1121 TYR 0.015 0.001 TYR B1067 ARG 0.011 0.000 ARG O 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 100 average time/residue: 0.4368 time to fit residues: 79.2364 Evaluate side-chains 84 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 4.324 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3405 time to fit residues: 9.4211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.0870 chunk 393 optimal weight: 0.9990 chunk 358 optimal weight: 50.0000 chunk 382 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 166 optimal weight: 0.4980 chunk 300 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 345 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 381 optimal weight: 8.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 965 GLN A1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34272 Z= 0.131 Angle : 0.522 9.614 46669 Z= 0.264 Chirality : 0.043 0.300 5400 Planarity : 0.004 0.070 6011 Dihedral : 6.841 114.384 5156 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.24 % Allowed : 15.84 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.69 (0.13), residues: 4233 helix: 2.17 (0.21), residues: 650 sheet: -0.21 (0.14), residues: 1341 loop : -1.46 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS A1048 PHE 0.015 0.001 PHE C 456 TYR 0.012 0.001 TYR O 41 ARG 0.005 0.000 ARG X 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 3.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 90 average time/residue: 0.4333 time to fit residues: 70.1137 Evaluate side-chains 85 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 3.576 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3050 time to fit residues: 7.9633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 4.9990 chunk 404 optimal weight: 30.0000 chunk 246 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 424 optimal weight: 6.9990 chunk 390 optimal weight: 5.9990 chunk 337 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 965 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34272 Z= 0.304 Angle : 0.585 9.673 46669 Z= 0.299 Chirality : 0.044 0.375 5400 Planarity : 0.004 0.069 6011 Dihedral : 7.266 118.618 5156 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.14 % Allowed : 16.03 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.85 (0.13), residues: 4233 helix: 1.82 (0.21), residues: 656 sheet: -0.28 (0.14), residues: 1339 loop : -1.51 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 171 HIS 0.004 0.001 HIS B1048 PHE 0.017 0.001 PHE B1121 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG X 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.4781 time to fit residues: 65.3232 Evaluate side-chains 74 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 3.692 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3010 time to fit residues: 7.9450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 9.9990 chunk 360 optimal weight: 40.0000 chunk 103 optimal weight: 0.7980 chunk 311 optimal weight: 40.0000 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 347 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.085349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056749 restraints weight = 214005.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.051146 restraints weight = 100135.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.051377 restraints weight = 63696.407| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34272 Z= 0.225 Angle : 0.555 11.216 46669 Z= 0.282 Chirality : 0.044 0.356 5400 Planarity : 0.004 0.070 6011 Dihedral : 7.188 117.461 5156 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.16 % Allowed : 16.11 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -0.79 (0.13), residues: 4233 helix: 1.88 (0.21), residues: 657 sheet: -0.24 (0.14), residues: 1333 loop : -1.48 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS B1048 PHE 0.013 0.001 PHE B1121 TYR 0.015 0.001 TYR O 41 ARG 0.009 0.000 ARG O 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5167.75 seconds wall clock time: 97 minutes 4.03 seconds (5824.03 seconds total)