Starting phenix.real_space_refine on Sat Mar 16 06:06:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tla_41366/03_2024/8tla_41366_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tla_41366/03_2024/8tla_41366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tla_41366/03_2024/8tla_41366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tla_41366/03_2024/8tla_41366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tla_41366/03_2024/8tla_41366_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tla_41366/03_2024/8tla_41366_trim_updated.pdb" } resolution = 3.2 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= 0.036 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 417 5.16 5 C 41490 2.51 5 N 11086 2.21 5 O 12044 1.98 5 H 65349 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A GLU 1000": "OE1" <-> "OE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A GLU 1087": "OE1" <-> "OE2" Residue "A PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A GLU 1122": "OE1" <-> "OE2" Residue "A GLU 1125": "OE1" <-> "OE2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A PHE 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1338": "OD1" <-> "OD2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A GLU 1377": "OE1" <-> "OE2" Residue "A GLU 1394": "OE1" <-> "OE2" Residue "A ASP 1404": "OD1" <-> "OD2" Residue "A GLU 1427": "OE1" <-> "OE2" Residue "A GLU 1430": "OE1" <-> "OE2" Residue "A ASP 1543": "OD1" <-> "OD2" Residue "A ASP 1619": "OD1" <-> "OD2" Residue "A GLU 1625": "OE1" <-> "OE2" Residue "A GLU 1633": "OE1" <-> "OE2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A GLU 1656": "OE1" <-> "OE2" Residue "A GLU 1659": "OE1" <-> "OE2" Residue "A TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A PHE 1750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1954": "OE1" <-> "OE2" Residue "A GLU 1963": "OE1" <-> "OE2" Residue "A TYR 1984": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 2027": "OD1" <-> "OD2" Residue "A GLU 2118": "OE1" <-> "OE2" Residue "A GLU 2134": "OE1" <-> "OE2" Residue "A GLU 2149": "OE1" <-> "OE2" Residue "A GLU 2160": "OE1" <-> "OE2" Residue "A ASP 2162": "OD1" <-> "OD2" Residue "A PHE 2172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 2173": "OD1" <-> "OD2" Residue "A PHE 2197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2338": "OE1" <-> "OE2" Residue "A PHE 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 2350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2352": "OE1" <-> "OE2" Residue "A PHE 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 2456": "OD1" <-> "OD2" Residue "A GLU 2544": "OE1" <-> "OE2" Residue "A ASP 2546": "OD1" <-> "OD2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 750": "OE1" <-> "OE2" Residue "B GLU 767": "OE1" <-> "OE2" Residue "B PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 814": "OD1" <-> "OD2" Residue "B TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 838": "OE1" <-> "OE2" Residue "B GLU 854": "OE1" <-> "OE2" Residue "B PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1049": "OD1" <-> "OD2" Residue "B TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1357": "OE1" <-> "OE2" Residue "B GLU 1442": "OE1" <-> "OE2" Residue "B ASP 1543": "OD1" <-> "OD2" Residue "B GLU 1603": "OE1" <-> "OE2" Residue "B ASP 1619": "OD1" <-> "OD2" Residue "B GLU 1639": "OE1" <-> "OE2" Residue "B GLU 1656": "OE1" <-> "OE2" Residue "B GLU 1658": "OE1" <-> "OE2" Residue "B TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1799": "OE1" <-> "OE2" Residue "B ASP 1887": "OD1" <-> "OD2" Residue "B PHE 1891": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1954": "OE1" <-> "OE2" Residue "B ASP 1968": "OD1" <-> "OD2" Residue "B GLU 2011": "OE1" <-> "OE2" Residue "B GLU 2014": "OE1" <-> "OE2" Residue "B ASP 2027": "OD1" <-> "OD2" Residue "B GLU 2043": "OE1" <-> "OE2" Residue "B GLU 2048": "OE1" <-> "OE2" Residue "B GLU 2125": "OE1" <-> "OE2" Residue "B GLU 2134": "OE1" <-> "OE2" Residue "B GLU 2149": "OE1" <-> "OE2" Residue "B GLU 2160": "OE1" <-> "OE2" Residue "B GLU 2163": "OE1" <-> "OE2" Residue "B PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 2350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2478": "OD1" <-> "OD2" Residue "B ASP 2549": "OD1" <-> "OD2" Residue "B PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C ASP 593": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C ASP 658": "OD1" <-> "OD2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C ASP 758": "OD1" <-> "OD2" Residue "C ASP 787": "OD1" <-> "OD2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C PHE 851": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1000": "OE1" <-> "OE2" Residue "C GLU 1033": "OE1" <-> "OE2" Residue "C GLU 1046": "OE1" <-> "OE2" Residue "C ASP 1049": "OD1" <-> "OD2" Residue "C GLU 1050": "OE1" <-> "OE2" Residue "C ASP 1066": "OD1" <-> "OD2" Residue "C GLU 1125": "OE1" <-> "OE2" Residue "C GLU 1262": "OE1" <-> "OE2" Residue "C ASP 1330": "OD1" <-> "OD2" Residue "C ASP 1347": "OD1" <-> "OD2" Residue "C ASP 1474": "OD1" <-> "OD2" Residue "C GLU 1630": "OE1" <-> "OE2" Residue "C ASP 1653": "OD1" <-> "OD2" Residue "C TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1729": "OD1" <-> "OD2" Residue "C GLU 1752": "OE1" <-> "OE2" Residue "C ASP 1887": "OD1" <-> "OD2" Residue "C GLU 1906": "OE1" <-> "OE2" Residue "C TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1946": "OE1" <-> "OE2" Residue "C ASP 1968": "OD1" <-> "OD2" Residue "C ASP 1977": "OD1" <-> "OD2" Residue "C GLU 2024": "OE1" <-> "OE2" Residue "C ASP 2027": "OD1" <-> "OD2" Residue "C GLU 2125": "OE1" <-> "OE2" Residue "C GLU 2134": "OE1" <-> "OE2" Residue "C GLU 2150": "OE1" <-> "OE2" Residue "C ASP 2162": "OD1" <-> "OD2" Residue "C GLU 2163": "OE1" <-> "OE2" Residue "C ASP 2173": "OD1" <-> "OD2" Residue "C GLU 2183": "OE1" <-> "OE2" Residue "C TYR 2225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 2456": "OD1" <-> "OD2" Residue "C ASP 2478": "OD1" <-> "OD2" Residue "C ASP 2486": "OD1" <-> "OD2" Residue "C PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2526": "OE1" <-> "OE2" Residue "C ASP 2546": "OD1" <-> "OD2" Residue "C ASP 2582": "OD1" <-> "OD2" Residue "D ASP 593": "OD1" <-> "OD2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 750": "OE1" <-> "OE2" Residue "D ASP 758": "OD1" <-> "OD2" Residue "D GLU 792": "OE1" <-> "OE2" Residue "D ASP 825": "OD1" <-> "OD2" Residue "D ASP 839": "OD1" <-> "OD2" Residue "D PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1006": "OD1" <-> "OD2" Residue "D PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1026": "OD1" <-> "OD2" Residue "D GLU 1030": "OE1" <-> "OE2" Residue "D GLU 1033": "OE1" <-> "OE2" Residue "D PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1049": "OD1" <-> "OD2" Residue "D ASP 1066": "OD1" <-> "OD2" Residue "D ASP 1129": "OD1" <-> "OD2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D ASP 1215": "OD1" <-> "OD2" Residue "D GLU 1260": "OE1" <-> "OE2" Residue "D TYR 1272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1324": "OE1" <-> "OE2" Residue "D PHE 1335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1543": "OD1" <-> "OD2" Residue "D ASP 1545": "OD1" <-> "OD2" Residue "D TYR 1588": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1619": "OD1" <-> "OD2" Residue "D GLU 1633": "OE1" <-> "OE2" Residue "D GLU 1639": "OE1" <-> "OE2" Residue "D GLU 1656": "OE1" <-> "OE2" Residue "D ASP 1681": "OD1" <-> "OD2" Residue "D PHE 1750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1762": "OD1" <-> "OD2" Residue "D ASP 1912": "OD1" <-> "OD2" Residue "D GLU 1931": "OE1" <-> "OE2" Residue "D ASP 1977": "OD1" <-> "OD2" Residue "D TYR 1984": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2125": "OE1" <-> "OE2" Residue "D ASP 2130": "OD1" <-> "OD2" Residue "D ASP 2173": "OD1" <-> "OD2" Residue "D PHE 2177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 2225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2338": "OE1" <-> "OE2" Residue "D PHE 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 2400": "OD1" <-> "OD2" Residue "D ASP 2456": "OD1" <-> "OD2" Residue "D ASP 2486": "OD1" <-> "OD2" Residue "D GLU 2531": "OE1" <-> "OE2" Residue "D GLU 2544": "OE1" <-> "OE2" Residue "D ASP 2582": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 130418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 32350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1989, 32350 Classifications: {'peptide': 1989} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1933} Chain breaks: 13 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 32312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1987, 32312 Classifications: {'peptide': 1987} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1931} Chain breaks: 13 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 32571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2004, 32571 Classifications: {'peptide': 2004} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1948} Chain breaks: 12 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 32957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 32957 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 2, 'PTRANS': 56, 'TRANS': 1975} Chain breaks: 11 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31094 SG CYS A2538 137.873 136.668 96.294 1.00 83.93 S ATOM 31143 SG CYS A2541 135.715 138.357 93.592 1.00 62.92 S ATOM 63406 SG CYS B2538 113.514 151.924 95.353 1.00 85.97 S ATOM 63455 SG CYS B2541 111.897 149.420 92.938 1.00 77.35 S ATOM 95977 SG CYS C2538 98.463 127.574 96.163 1.00 82.66 S ATOM 96026 SG CYS C2541 101.024 126.202 93.671 1.00 88.31 S ATOM A0MBQ SG CYS D2538 122.528 112.460 97.353 1.00 84.30 S ATOM A0MD3 SG CYS D2541 124.141 114.912 94.870 1.00 73.96 S Time building chain proxies: 40.14, per 1000 atoms: 0.31 Number of scatterers: 130418 At special positions: 0 Unit cell: (240.366, 251.93, 181.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 417 16.00 P 24 15.00 O 12044 8.00 N 11086 7.00 C 41490 6.00 H 65349 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 79.55 Conformation dependent library (CDL) restraints added in 9.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2541 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2538 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B3001 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2541 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2538 " pdb=" ZN C3001 " pdb="ZN ZN C3001 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C3001 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2541 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2538 " pdb=" ZN D3001 " pdb="ZN ZN D3001 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D3001 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2541 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2538 " Number of angles added : 4 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15390 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 402 helices and 30 sheets defined 76.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 48.84 Creating SS restraints... Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.679A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 277' Processing helix chain 'A' and resid 362 through 367 removed outlier: 4.239A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N PHE A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 367' Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.710A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 514 through 527 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 537 through 542 removed outlier: 4.542A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 565 Proline residue: A 548 - end of helix Processing helix chain 'A' and resid 567 through 578 removed outlier: 3.709A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 5.679A pdb=" N GLY A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 603 removed outlier: 3.589A pdb=" N ASN A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 627 through 640 removed outlier: 4.472A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 658 through 666 removed outlier: 3.855A pdb=" N SER A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 658 through 666' Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 719 through 741 Processing helix chain 'A' and resid 744 through 756 removed outlier: 3.939A pdb=" N ASP A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.796A pdb=" N ASN A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 831 removed outlier: 4.498A pdb=" N LYS A 829 " --> pdb=" O ASP A 825 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 848 removed outlier: 5.324A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 874 removed outlier: 3.606A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 3.750A pdb=" N ARG A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 1002 Processing helix chain 'A' and resid 1024 through 1037 Processing helix chain 'A' and resid 1052 through 1066 removed outlier: 3.525A pdb=" N MET A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A1065 " --> pdb=" O HIS A1061 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ASP A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.775A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 Processing helix chain 'A' and resid 1100 through 1128 removed outlier: 5.271A pdb=" N GLU A1125 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 3.659A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 Processing helix chain 'A' and resid 1202 through 1212 Processing helix chain 'A' and resid 1218 through 1237 Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 3.506A pdb=" N LEU A1245 " --> pdb=" O GLY A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 Processing helix chain 'A' and resid 1271 through 1278 Processing helix chain 'A' and resid 1279 through 1293 Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 4.663A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 Processing helix chain 'A' and resid 1338 through 1353 Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 5.658A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.820A pdb=" N LYS A1386 " --> pdb=" O TYR A1382 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1393 through 1402 Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1428 through 1434 removed outlier: 4.113A pdb=" N TYR A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1458 Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 4.056A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1489 removed outlier: 4.630A pdb=" N ASN A1487 " --> pdb=" O PRO A1483 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR A1489 " --> pdb=" O SER A1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1483 through 1489' Processing helix chain 'A' and resid 1490 through 1512 removed outlier: 5.777A pdb=" N THR A1496 " --> pdb=" O GLN A1492 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE A1497 " --> pdb=" O THR A1493 " (cutoff:3.500A) Proline residue: A1512 - end of helix Processing helix chain 'A' and resid 1516 through 1534 Processing helix chain 'A' and resid 1541 through 1557 Processing helix chain 'A' and resid 1587 through 1624 Proline residue: A1608 - end of helix removed outlier: 3.911A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1616 " --> pdb=" O ALA A1612 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A1617 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 removed outlier: 3.628A pdb=" N GLY A1641 " --> pdb=" O ARG A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1655 Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 5.348A pdb=" N LYS A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1695 Processing helix chain 'A' and resid 1718 through 1732 Processing helix chain 'A' and resid 1733 through 1744 Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1765 through 1779 Processing helix chain 'A' and resid 1781 through 1807 Processing helix chain 'A' and resid 1864 through 1882 removed outlier: 3.854A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1895 removed outlier: 3.531A pdb=" N ARG A1893 " --> pdb=" O GLN A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1916 Processing helix chain 'A' and resid 1917 through 1923 Processing helix chain 'A' and resid 1924 through 1929 Processing helix chain 'A' and resid 1930 through 1949 removed outlier: 4.527A pdb=" N GLY A1935 " --> pdb=" O GLU A1931 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU A1936 " --> pdb=" O ASP A1932 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1962 Processing helix chain 'A' and resid 1965 through 1976 removed outlier: 3.687A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A1974 " --> pdb=" O ILE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1985 removed outlier: 3.589A pdb=" N LYS A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 removed outlier: 3.565A pdb=" N MET A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2021 removed outlier: 3.974A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2037 removed outlier: 4.489A pdb=" N GLU A2037 " --> pdb=" O TYR A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2065 removed outlier: 3.901A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A2064 " --> pdb=" O LEU A2060 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS A2065 " --> pdb=" O SER A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2072 Processing helix chain 'A' and resid 2112 through 2121 Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 4.280A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A2147 " --> pdb=" O ILE A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2141 through 2147' Processing helix chain 'A' and resid 2148 through 2158 Processing helix chain 'A' and resid 2167 through 2192 removed outlier: 4.430A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A2191 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Proline residue: A2192 - end of helix Processing helix chain 'A' and resid 2193 through 2201 removed outlier: 3.762A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2223 Processing helix chain 'A' and resid 2261 through 2276 Processing helix chain 'A' and resid 2277 through 2310 removed outlier: 6.157A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A2310 " --> pdb=" O THR A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2317 Processing helix chain 'A' and resid 2318 through 2336 Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 4.741A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU A2353 " --> pdb=" O ILE A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2364 removed outlier: 3.525A pdb=" N SER A2361 " --> pdb=" O ASN A2357 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2390 Processing helix chain 'A' and resid 2457 through 2472 removed outlier: 4.044A pdb=" N LEU A2470 " --> pdb=" O MET A2466 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A2471 " --> pdb=" O ASN A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.580A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A2480 " --> pdb=" O VAL A2476 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2475 through 2481' Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2537 removed outlier: 3.658A pdb=" N ILE A2512 " --> pdb=" O VAL A2508 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2549 removed outlier: 4.195A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A2549 " --> pdb=" O ARG A2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2544 through 2549' Processing helix chain 'A' and resid 2554 through 2561 Processing helix chain 'A' and resid 2564 through 2578 Processing helix chain 'A' and resid 2584 through 2597 Processing helix chain 'A' and resid 2607 through 2612 Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.670A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 277' Processing helix chain 'B' and resid 362 through 367 removed outlier: 4.240A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N PHE B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 367' Processing helix chain 'B' and resid 435 through 462 removed outlier: 3.763A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 514 through 527 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.620A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 565 Processing helix chain 'B' and resid 567 through 578 removed outlier: 3.846A pdb=" N LYS B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 585 Processing helix chain 'B' and resid 590 through 603 removed outlier: 3.901A pdb=" N ARG B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 611 through 626 removed outlier: 3.523A pdb=" N VAL B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 640 removed outlier: 4.242A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 658 Processing helix chain 'B' and resid 659 through 666 removed outlier: 4.839A pdb=" N ASP B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 659 through 666' Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 719 through 741 Processing helix chain 'B' and resid 744 through 756 removed outlier: 3.806A pdb=" N ILE B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 766 removed outlier: 3.855A pdb=" N ASP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 785 Processing helix chain 'B' and resid 811 through 820 removed outlier: 3.668A pdb=" N ASP B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 831 removed outlier: 3.502A pdb=" N PHE B 830 " --> pdb=" O LYS B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 848 removed outlier: 5.309A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 874 removed outlier: 3.638A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 removed outlier: 3.805A pdb=" N ARG B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 887 " --> pdb=" O ARG B 883 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 1002 Processing helix chain 'B' and resid 1024 through 1037 Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 5.290A pdb=" N ASP B1066 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.722A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 Processing helix chain 'B' and resid 1100 through 1128 removed outlier: 4.762A pdb=" N GLU B1125 " --> pdb=" O VAL B1121 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU B1126 " --> pdb=" O GLU B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.217A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1201 Processing helix chain 'B' and resid 1202 through 1212 Processing helix chain 'B' and resid 1218 through 1237 Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 3.583A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1271 through 1278 Processing helix chain 'B' and resid 1279 through 1293 removed outlier: 3.782A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1309 removed outlier: 3.607A pdb=" N LYS B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 Processing helix chain 'B' and resid 1338 through 1353 Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 5.213A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1392 Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1402 Processing helix chain 'B' and resid 1406 through 1421 Processing helix chain 'B' and resid 1428 through 1434 removed outlier: 4.568A pdb=" N TYR B1432 " --> pdb=" O MET B1428 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1458 Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 4.070A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1483 through 1488 removed outlier: 4.161A pdb=" N ASN B1487 " --> pdb=" O PRO B1483 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1483 through 1488' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 3.836A pdb=" N THR B1493 " --> pdb=" O THR B1489 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1512 Proline residue: B1512 - end of helix Processing helix chain 'B' and resid 1516 through 1534 Processing helix chain 'B' and resid 1541 through 1557 Processing helix chain 'B' and resid 1587 through 1624 Proline residue: B1608 - end of helix removed outlier: 3.987A pdb=" N LEU B1617 " --> pdb=" O GLU B1613 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B1618 " --> pdb=" O LEU B1614 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B1619 " --> pdb=" O SER B1615 " (cutoff:3.500A) Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 removed outlier: 3.649A pdb=" N GLN B1636 " --> pdb=" O SER B1632 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B1637 " --> pdb=" O GLU B1633 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1658 removed outlier: 4.944A pdb=" N GLU B1656 " --> pdb=" O LYS B1652 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B1657 " --> pdb=" O ASP B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1675 removed outlier: 5.229A pdb=" N LYS B1675 " --> pdb=" O GLN B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1695 Processing helix chain 'B' and resid 1718 through 1732 Processing helix chain 'B' and resid 1733 through 1744 Processing helix chain 'B' and resid 1746 through 1762 Processing helix chain 'B' and resid 1765 through 1779 Processing helix chain 'B' and resid 1781 through 1807 Processing helix chain 'B' and resid 1864 through 1882 removed outlier: 3.673A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1885 through 1894 removed outlier: 3.629A pdb=" N ARG B1893 " --> pdb=" O GLN B1889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1902 through 1916 Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 3.718A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 5.142A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1931 through 1949 removed outlier: 4.427A pdb=" N GLY B1935 " --> pdb=" O GLU B1931 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU B1936 " --> pdb=" O ASP B1932 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1962 Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 3.901A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B1974 " --> pdb=" O ILE B1970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1985 removed outlier: 4.423A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 Processing helix chain 'B' and resid 2010 through 2021 removed outlier: 3.757A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2036 removed outlier: 3.877A pdb=" N TYR B2033 " --> pdb=" O ILE B2029 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B2034 " --> pdb=" O LYS B2030 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2062 removed outlier: 3.532A pdb=" N VAL B2049 " --> pdb=" O SER B2045 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2073 Proline residue: B2073 - end of helix Processing helix chain 'B' and resid 2112 through 2121 Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 4.357A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B2147 " --> pdb=" O ILE B2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2141 through 2147' Processing helix chain 'B' and resid 2148 through 2158 Processing helix chain 'B' and resid 2167 through 2192 removed outlier: 4.364A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B2191 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Proline residue: B2192 - end of helix Processing helix chain 'B' and resid 2193 through 2223 removed outlier: 3.751A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) Processing helix chain 'B' and resid 2261 through 2276 Processing helix chain 'B' and resid 2277 through 2310 removed outlier: 6.638A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B2310 " --> pdb=" O THR B2306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2318 removed outlier: 5.673A pdb=" N MET B2318 " --> pdb=" O MET B2314 " (cutoff:3.500A) Processing helix chain 'B' and resid 2319 through 2336 Processing helix chain 'B' and resid 2339 through 2353 removed outlier: 4.918A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B2353 " --> pdb=" O ILE B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2364 removed outlier: 3.545A pdb=" N SER B2361 " --> pdb=" O ASN B2357 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2390 Processing helix chain 'B' and resid 2457 through 2472 removed outlier: 4.021A pdb=" N LEU B2470 " --> pdb=" O MET B2466 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B2471 " --> pdb=" O ASN B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.309A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2537 removed outlier: 3.951A pdb=" N ILE B2512 " --> pdb=" O VAL B2508 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.517A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP B2549 " --> pdb=" O ARG B2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2544 through 2549' Processing helix chain 'B' and resid 2554 through 2561 Processing helix chain 'B' and resid 2564 through 2578 Processing helix chain 'B' and resid 2584 through 2597 Processing helix chain 'B' and resid 2607 through 2612 Processing helix chain 'B' and resid 2598 through 2603 removed outlier: 4.558A pdb=" N TRP B2601 " --> pdb=" O ASN B2598 " (cutoff:3.500A) Proline residue: B2603 - end of helix Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.662A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 277' Processing helix chain 'C' and resid 362 through 367 removed outlier: 4.240A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 367' Processing helix chain 'C' and resid 435 through 462 removed outlier: 3.698A pdb=" N ILE C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'C' and resid 514 through 527 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 537 through 542 removed outlier: 4.636A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 565 removed outlier: 3.625A pdb=" N ALA C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) Proline residue: C 548 - end of helix removed outlier: 3.564A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 removed outlier: 3.820A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 585 Processing helix chain 'C' and resid 590 through 603 removed outlier: 3.733A pdb=" N ASN C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 627 through 640 removed outlier: 4.323A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 Processing helix chain 'C' and resid 658 through 666 removed outlier: 3.823A pdb=" N SER C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ASP C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 658 through 666' Processing helix chain 'C' and resid 682 through 689 removed outlier: 3.519A pdb=" N GLU C 689 " --> pdb=" O ILE C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 719 through 741 Processing helix chain 'C' and resid 744 through 756 removed outlier: 4.428A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 766 Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 802 through 807 Proline residue: C 807 - end of helix Processing helix chain 'C' and resid 811 through 821 removed outlier: 4.028A pdb=" N ALA C 821 " --> pdb=" O SER C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.793A pdb=" N LYS C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 828 " --> pdb=" O ASP C 824 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 829 " --> pdb=" O ASP C 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 830 " --> pdb=" O LYS C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 848 removed outlier: 5.623A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 874 removed outlier: 3.726A pdb=" N LYS C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 removed outlier: 3.773A pdb=" N ARG C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 887 " --> pdb=" O ARG C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 1002 Processing helix chain 'C' and resid 1024 through 1037 removed outlier: 3.565A pdb=" N MET C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1066 removed outlier: 3.746A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASP C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.685A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1095 Processing helix chain 'C' and resid 1100 through 1128 removed outlier: 3.535A pdb=" N SER C1124 " --> pdb=" O MET C1120 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU C1125 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU C1126 " --> pdb=" O GLU C1122 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP C1127 " --> pdb=" O LYS C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 3.641A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1201 Processing helix chain 'C' and resid 1202 through 1212 Processing helix chain 'C' and resid 1218 through 1237 Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 3.774A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 Processing helix chain 'C' and resid 1271 through 1278 Processing helix chain 'C' and resid 1279 through 1293 removed outlier: 3.806A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 4.317A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 Processing helix chain 'C' and resid 1338 through 1353 Processing helix chain 'C' and resid 1360 through 1377 Processing helix chain 'C' and resid 1380 through 1391 removed outlier: 3.623A pdb=" N LYS C1386 " --> pdb=" O TYR C1382 " (cutoff:3.500A) Processing helix chain 'C' and resid 1392 through 1402 removed outlier: 4.257A pdb=" N HIS C1402 " --> pdb=" O SER C1398 " (cutoff:3.500A) Processing helix chain 'C' and resid 1406 through 1420 Processing helix chain 'C' and resid 1428 through 1458 removed outlier: 4.116A pdb=" N TYR C1432 " --> pdb=" O MET C1428 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASN C1435 " --> pdb=" O ILE C1431 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N HIS C1436 " --> pdb=" O TYR C1432 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE C1437 " --> pdb=" O THR C1433 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP C1438 " --> pdb=" O SER C1434 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.712A pdb=" N VAL C1471 " --> pdb=" O TYR C1467 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 1490 through 1512 removed outlier: 5.032A pdb=" N THR C1496 " --> pdb=" O GLN C1492 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE C1497 " --> pdb=" O THR C1493 " (cutoff:3.500A) Proline residue: C1512 - end of helix Processing helix chain 'C' and resid 1515 through 1537 Processing helix chain 'C' and resid 1542 through 1557 Processing helix chain 'C' and resid 1587 through 1624 Proline residue: C1608 - end of helix removed outlier: 4.196A pdb=" N LEU C1617 " --> pdb=" O GLU C1613 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C1618 " --> pdb=" O LEU C1614 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C1619 " --> pdb=" O SER C1615 " (cutoff:3.500A) Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 Processing helix chain 'C' and resid 1642 through 1658 removed outlier: 4.872A pdb=" N GLU C1656 " --> pdb=" O LYS C1652 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C1657 " --> pdb=" O ASP C1653 " (cutoff:3.500A) Processing helix chain 'C' and resid 1659 through 1675 removed outlier: 5.249A pdb=" N LYS C1675 " --> pdb=" O GLN C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1695 Processing helix chain 'C' and resid 1718 through 1732 Processing helix chain 'C' and resid 1733 through 1744 Processing helix chain 'C' and resid 1746 through 1762 Processing helix chain 'C' and resid 1765 through 1779 Processing helix chain 'C' and resid 1781 through 1807 Processing helix chain 'C' and resid 1864 through 1882 removed outlier: 3.787A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1885 through 1894 removed outlier: 3.620A pdb=" N ARG C1893 " --> pdb=" O GLN C1889 " (cutoff:3.500A) Processing helix chain 'C' and resid 1902 through 1916 Processing helix chain 'C' and resid 1917 through 1923 Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 5.152A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1931 through 1949 removed outlier: 4.657A pdb=" N GLY C1935 " --> pdb=" O GLU C1931 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU C1936 " --> pdb=" O ASP C1932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1962 Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 4.004A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1985 removed outlier: 4.297A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 Processing helix chain 'C' and resid 2010 through 2021 removed outlier: 4.131A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2037 removed outlier: 4.448A pdb=" N GLU C2037 " --> pdb=" O TYR C2033 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2062 removed outlier: 3.884A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) Processing helix chain 'C' and resid 2064 through 2072 Processing helix chain 'C' and resid 2112 through 2121 Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 4.213A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU C2147 " --> pdb=" O ILE C2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2141 through 2147' Processing helix chain 'C' and resid 2148 through 2159 Processing helix chain 'C' and resid 2167 through 2192 removed outlier: 4.442A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) Proline residue: C2192 - end of helix Processing helix chain 'C' and resid 2193 through 2201 removed outlier: 3.736A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) Processing helix chain 'C' and resid 2202 through 2222 Processing helix chain 'C' and resid 2261 through 2276 Processing helix chain 'C' and resid 2277 through 2310 removed outlier: 6.549A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C2310 " --> pdb=" O THR C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2317 Processing helix chain 'C' and resid 2318 through 2336 Processing helix chain 'C' and resid 2339 through 2353 removed outlier: 4.934A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU C2353 " --> pdb=" O ILE C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2364 removed outlier: 3.552A pdb=" N SER C2361 " --> pdb=" O ASN C2357 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2390 Processing helix chain 'C' and resid 2391 through 2396 removed outlier: 3.912A pdb=" N PHE C2395 " --> pdb=" O LEU C2391 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE C2396 " --> pdb=" O LYS C2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2391 through 2396' Processing helix chain 'C' and resid 2457 through 2472 removed outlier: 4.114A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG C2471 " --> pdb=" O ASN C2467 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.169A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2537 removed outlier: 3.939A pdb=" N ILE C2512 " --> pdb=" O VAL C2508 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.274A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2544 through 2549' Processing helix chain 'C' and resid 2554 through 2561 Processing helix chain 'C' and resid 2564 through 2578 Processing helix chain 'C' and resid 2584 through 2597 Processing helix chain 'C' and resid 2607 through 2612 Processing helix chain 'C' and resid 2598 through 2603 removed outlier: 4.718A pdb=" N TRP C2601 " --> pdb=" O ASN C2598 " (cutoff:3.500A) Proline residue: C2603 - end of helix Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.701A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 277' Processing helix chain 'D' and resid 362 through 367 removed outlier: 4.235A pdb=" N LEU D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE D 367 " --> pdb=" O ILE D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 362 through 367' Processing helix chain 'D' and resid 435 through 462 Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 514 through 527 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 537 through 544 removed outlier: 4.585A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP D 543 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 565 removed outlier: 4.785A pdb=" N TYR D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 removed outlier: 3.920A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 586 removed outlier: 5.190A pdb=" N GLY D 586 " --> pdb=" O GLN D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 603 removed outlier: 3.770A pdb=" N THR D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 610 Processing helix chain 'D' and resid 611 through 626 Processing helix chain 'D' and resid 627 through 640 removed outlier: 3.746A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 658 Processing helix chain 'D' and resid 659 through 666 removed outlier: 5.098A pdb=" N ASP D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 659 through 666' Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 719 through 741 Processing helix chain 'D' and resid 744 through 756 removed outlier: 4.125A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 756 " --> pdb=" O SER D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 766 removed outlier: 3.765A pdb=" N CYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 784 Processing helix chain 'D' and resid 811 through 820 removed outlier: 3.527A pdb=" N ASP D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 831 removed outlier: 4.267A pdb=" N LYS D 829 " --> pdb=" O ASP D 825 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 830 " --> pdb=" O LYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 848 removed outlier: 5.493A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 874 removed outlier: 3.613A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 removed outlier: 3.567A pdb=" N ARG D 886 " --> pdb=" O LEU D 882 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 887 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 1003 Proline residue: D1003 - end of helix Processing helix chain 'D' and resid 1024 through 1037 Processing helix chain 'D' and resid 1052 through 1066 removed outlier: 5.607A pdb=" N ASP D1066 " --> pdb=" O LEU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.747A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 3.706A pdb=" N SER D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLU D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU D1126 " --> pdb=" O GLU D1122 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TRP D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 3.600A pdb=" N CYS D1183 " --> pdb=" O LEU D1179 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1201 removed outlier: 3.600A pdb=" N LYS D1192 " --> pdb=" O GLN D1188 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1212 Processing helix chain 'D' and resid 1218 through 1237 removed outlier: 3.796A pdb=" N MET D1222 " --> pdb=" O ASP D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 3.965A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 removed outlier: 3.962A pdb=" N ALA D1261 " --> pdb=" O GLY D1257 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU D1262 " --> pdb=" O LEU D1258 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D1263 " --> pdb=" O LEU D1259 " (cutoff:3.500A) Processing helix chain 'D' and resid 1271 through 1278 removed outlier: 3.631A pdb=" N GLU D1277 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1296 through 1309 removed outlier: 4.590A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D1302 " --> pdb=" O GLN D1298 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D1303 " --> pdb=" O TYR D1299 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.693A pdb=" N MET D1322 " --> pdb=" O GLN D1318 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 Processing helix chain 'D' and resid 1360 through 1377 Processing helix chain 'D' and resid 1380 through 1392 removed outlier: 3.916A pdb=" N LYS D1386 " --> pdb=" O TYR D1382 " (cutoff:3.500A) Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1393 through 1402 removed outlier: 3.723A pdb=" N HIS D1402 " --> pdb=" O SER D1398 " (cutoff:3.500A) Processing helix chain 'D' and resid 1406 through 1420 Processing helix chain 'D' and resid 1428 through 1434 removed outlier: 4.117A pdb=" N TYR D1432 " --> pdb=" O MET D1428 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1458 removed outlier: 3.530A pdb=" N THR D1439 " --> pdb=" O ASN D1435 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 5.164A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 4.648A pdb=" N THR D1493 " --> pdb=" O THR D1489 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1512 removed outlier: 3.969A pdb=" N GLN D1500 " --> pdb=" O THR D1496 " (cutoff:3.500A) Proline residue: D1512 - end of helix Processing helix chain 'D' and resid 1515 through 1537 removed outlier: 3.627A pdb=" N SER D1521 " --> pdb=" O GLN D1517 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1570 removed outlier: 3.631A pdb=" N ASP D1545 " --> pdb=" O PRO D1541 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D1546 " --> pdb=" O MET D1542 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D1552 " --> pdb=" O ILE D1548 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D1555 " --> pdb=" O MET D1551 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA D1556 " --> pdb=" O LEU D1552 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER D1567 " --> pdb=" O GLN D1563 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER D1568 " --> pdb=" O ARG D1564 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR D1569 " --> pdb=" O ASN D1565 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS D1570 " --> pdb=" O ALA D1566 " (cutoff:3.500A) Processing helix chain 'D' and resid 1588 through 1624 removed outlier: 4.235A pdb=" N ILE D1592 " --> pdb=" O TYR D1588 " (cutoff:3.500A) Proline residue: D1608 - end of helix removed outlier: 3.526A pdb=" N GLN D1611 " --> pdb=" O LYS D1607 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D1617 " --> pdb=" O GLU D1613 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D1618 " --> pdb=" O LEU D1614 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D1619 " --> pdb=" O SER D1615 " (cutoff:3.500A) Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 removed outlier: 3.771A pdb=" N GLY D1641 " --> pdb=" O ARG D1637 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1655 Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 5.167A pdb=" N LYS D1675 " --> pdb=" O GLN D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1695 Processing helix chain 'D' and resid 1718 through 1732 Processing helix chain 'D' and resid 1733 through 1744 Processing helix chain 'D' and resid 1746 through 1762 Processing helix chain 'D' and resid 1765 through 1779 Processing helix chain 'D' and resid 1781 through 1807 Processing helix chain 'D' and resid 1864 through 1882 removed outlier: 4.322A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1895 removed outlier: 3.718A pdb=" N ARG D1893 " --> pdb=" O GLN D1889 " (cutoff:3.500A) Processing helix chain 'D' and resid 1902 through 1916 Processing helix chain 'D' and resid 1917 through 1923 Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 3.591A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1931 through 1949 removed outlier: 4.659A pdb=" N GLY D1935 " --> pdb=" O GLU D1931 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU D1936 " --> pdb=" O ASP D1932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1962 Processing helix chain 'D' and resid 1965 through 1976 removed outlier: 3.950A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1978 through 1985 removed outlier: 4.464A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 Processing helix chain 'D' and resid 2010 through 2021 removed outlier: 3.833A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2040 removed outlier: 3.599A pdb=" N TYR D2033 " --> pdb=" O ILE D2029 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU D2037 " --> pdb=" O TYR D2033 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU D2038 " --> pdb=" O LEU D2034 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU D2040 " --> pdb=" O GLU D2036 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2065 removed outlier: 4.014A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN D2064 " --> pdb=" O LEU D2060 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS D2065 " --> pdb=" O SER D2061 " (cutoff:3.500A) Processing helix chain 'D' and resid 2066 through 2073 Proline residue: D2073 - end of helix Processing helix chain 'D' and resid 2112 through 2121 Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 4.230A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU D2147 " --> pdb=" O ILE D2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2141 through 2147' Processing helix chain 'D' and resid 2148 through 2159 Processing helix chain 'D' and resid 2167 through 2192 removed outlier: 4.360A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) Proline residue: D2192 - end of helix Processing helix chain 'D' and resid 2193 through 2222 removed outlier: 3.826A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP D2204 " --> pdb=" O ARG D2200 " (cutoff:3.500A) Processing helix chain 'D' and resid 2260 through 2276 removed outlier: 4.664A pdb=" N LEU D2264 " --> pdb=" O SER D2260 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2310 removed outlier: 6.413A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY D2310 " --> pdb=" O THR D2306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2317 Processing helix chain 'D' and resid 2318 through 2336 Processing helix chain 'D' and resid 2337 through 2353 removed outlier: 4.687A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU D2353 " --> pdb=" O ILE D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2364 removed outlier: 3.521A pdb=" N SER D2361 " --> pdb=" O ASN D2357 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2390 Processing helix chain 'D' and resid 2457 through 2472 removed outlier: 4.017A pdb=" N LEU D2470 " --> pdb=" O MET D2466 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG D2471 " --> pdb=" O ASN D2467 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2480 removed outlier: 4.236A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2537 removed outlier: 3.974A pdb=" N ILE D2512 " --> pdb=" O VAL D2508 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2549 removed outlier: 4.105A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP D2549 " --> pdb=" O ARG D2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2544 through 2549' Processing helix chain 'D' and resid 2554 through 2561 Processing helix chain 'D' and resid 2564 through 2578 Processing helix chain 'D' and resid 2584 through 2597 Processing helix chain 'D' and resid 2607 through 2612 Processing sheet with id= 1, first strand: chain 'A' and resid 252 through 255 Processing sheet with id= 2, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.512A pdb=" N ASN A 313 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE A 306 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 288 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 309 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU A 282 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 368 through 371 Processing sheet with id= 4, first strand: chain 'A' and resid 396 through 401 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'A' and resid 667 through 672 removed outlier: 4.226A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 800 through 803 Processing sheet with id= 7, first strand: chain 'A' and resid 2122 through 2128 removed outlier: 4.245A pdb=" N SER A2132 " --> pdb=" O ARG A2128 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 2395 through 2399 removed outlier: 7.259A pdb=" N PHE A2395 " --> pdb=" O ALA A2454 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N SER A2450 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 252 through 255 Processing sheet with id= 10, first strand: chain 'B' and resid 312 through 315 removed outlier: 4.506A pdb=" N ASN B 313 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 306 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 288 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 309 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU B 282 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 368 through 371 Processing sheet with id= 12, first strand: chain 'B' and resid 396 through 401 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'B' and resid 667 through 672 Processing sheet with id= 14, first strand: chain 'B' and resid 800 through 803 Processing sheet with id= 15, first strand: chain 'B' and resid 2122 through 2128 removed outlier: 4.307A pdb=" N SER B2132 " --> pdb=" O ARG B2128 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 2395 through 2399 removed outlier: 7.208A pdb=" N PHE B2395 " --> pdb=" O ALA B2454 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER B2450 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 252 through 255 Processing sheet with id= 18, first strand: chain 'C' and resid 312 through 315 removed outlier: 4.512A pdb=" N ASN C 313 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N PHE C 306 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 288 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 309 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU C 282 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 368 through 371 Processing sheet with id= 20, first strand: chain 'C' and resid 396 through 401 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'C' and resid 667 through 670 removed outlier: 3.915A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 2122 through 2128 removed outlier: 4.296A pdb=" N SER C2132 " --> pdb=" O ARG C2128 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 252 through 255 Processing sheet with id= 24, first strand: chain 'D' and resid 312 through 315 removed outlier: 4.498A pdb=" N ASN D 313 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE D 306 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 288 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 309 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU D 282 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 368 through 371 Processing sheet with id= 26, first strand: chain 'D' and resid 396 through 401 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'D' and resid 667 through 672 removed outlier: 3.998A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 800 through 803 Processing sheet with id= 29, first strand: chain 'D' and resid 2122 through 2128 removed outlier: 4.240A pdb=" N SER D2132 " --> pdb=" O ARG D2128 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 2395 through 2399 removed outlier: 7.058A pdb=" N PHE D2395 " --> pdb=" O ALA D2454 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER D2450 " --> pdb=" O VAL D2399 " (cutoff:3.500A) 4125 hydrogen bonds defined for protein. 12321 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: 55.01 Time building geometry restraints manager: 83.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 65200 1.03 - 1.23: 294 1.23 - 1.43: 27127 1.43 - 1.62: 38316 1.62 - 1.82: 681 Bond restraints: 131618 Sorted by residual: bond pdb=" CE LYS D1123 " pdb=" NZ LYS D1123 " ideal model delta sigma weight residual 1.489 1.440 0.049 3.00e-02 1.11e+03 2.71e+00 bond pdb=" CG1 ILE C2207 " pdb=" CD1 ILE C2207 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.95e+00 bond pdb=" CA ASN A 641 " pdb=" CB ASN A 641 " ideal model delta sigma weight residual 1.531 1.551 -0.020 1.51e-02 4.39e+03 1.84e+00 bond pdb=" CB LYS A1898 " pdb=" CG LYS A1898 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CB ARG D2524 " pdb=" CG ARG D2524 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 ... (remaining 131613 not shown) Histogram of bond angle deviations from ideal: 98.82 - 107.03: 2279 107.03 - 115.24: 166991 115.24 - 123.45: 58059 123.45 - 131.66: 10701 131.66 - 139.87: 82 Bond angle restraints: 238112 Sorted by residual: angle pdb=" CB LYS A1898 " pdb=" CG LYS A1898 " pdb=" CD LYS A1898 " ideal model delta sigma weight residual 111.30 121.09 -9.79 2.30e+00 1.89e-01 1.81e+01 angle pdb=" CB LYS C 608 " pdb=" CG LYS C 608 " pdb=" CD LYS C 608 " ideal model delta sigma weight residual 111.30 119.29 -7.99 2.30e+00 1.89e-01 1.21e+01 angle pdb=" N VAL B1333 " pdb=" CA VAL B1333 " pdb=" C VAL B1333 " ideal model delta sigma weight residual 106.21 109.39 -3.18 1.07e+00 8.73e-01 8.84e+00 angle pdb=" CA ASN A 641 " pdb=" CB ASN A 641 " pdb=" CG ASN A 641 " ideal model delta sigma weight residual 112.60 115.54 -2.94 1.00e+00 1.00e+00 8.66e+00 angle pdb=" C HIS B 783 " pdb=" N VAL B 784 " pdb=" CA VAL B 784 " ideal model delta sigma weight residual 122.35 118.91 3.44 1.18e+00 7.18e-01 8.51e+00 ... (remaining 238107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 57421 24.73 - 49.45: 3300 49.45 - 74.18: 699 74.18 - 98.91: 82 98.91 - 123.64: 16 Dihedral angle restraints: 61518 sinusoidal: 33803 harmonic: 27715 Sorted by residual: dihedral pdb=" C1 I3P B3002 " pdb=" C2 I3P B3002 " pdb=" C3 I3P B3002 " pdb=" C4 I3P B3002 " ideal model delta sinusoidal sigma weight residual 56.81 -66.83 123.64 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C4 I3P C3002 " pdb=" C2 I3P C3002 " pdb=" C3 I3P C3002 " pdb=" O2 I3P C3002 " ideal model delta sinusoidal sigma weight residual 65.28 -171.13 -123.59 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C1 I3P C3002 " pdb=" C2 I3P C3002 " pdb=" C3 I3P C3002 " pdb=" C4 I3P C3002 " ideal model delta sinusoidal sigma weight residual 56.81 -66.77 123.58 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 61515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 9192 0.058 - 0.116: 1034 0.116 - 0.174: 57 0.174 - 0.233: 4 0.233 - 0.291: 8 Chirality restraints: 10295 Sorted by residual: chirality pdb=" C3' ATP A3004 " pdb=" C2' ATP A3004 " pdb=" C4' ATP A3004 " pdb=" O3' ATP A3004 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' ATP C3004 " pdb=" C1' ATP C3004 " pdb=" C3' ATP C3004 " pdb=" O2' ATP C3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' ATP B3004 " pdb=" C1' ATP B3004 " pdb=" C3' ATP B3004 " pdb=" O2' ATP B3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 10292 not shown) Planarity restraints: 19074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C2131 " -0.246 9.50e-02 1.11e+02 8.25e-02 8.14e+00 pdb=" NE ARG C2131 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C2131 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C2131 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C2131 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C2131 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG C2131 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C2131 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C2131 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 788 " -0.197 9.50e-02 1.11e+02 6.59e-02 5.16e+00 pdb=" NE ARG A 788 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 788 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 788 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 788 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 788 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 788 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 788 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 788 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1468 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C VAL A1468 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A1468 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A1469 " 0.012 2.00e-02 2.50e+03 ... (remaining 19071 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 1540 2.06 - 2.70: 210965 2.70 - 3.33: 397261 3.33 - 3.97: 480041 3.97 - 4.60: 757237 Nonbonded interactions: 1847044 Sorted by model distance: nonbonded pdb=" O ASN D1022 " pdb="HD21 ASN D1022 " model vdw 1.429 1.850 nonbonded pdb=" OE1 GLU B1767 " pdb=" H GLU B1767 " model vdw 1.463 1.850 nonbonded pdb=" OE1 GLU C2024 " pdb=" H GLU C2024 " model vdw 1.489 1.850 nonbonded pdb=" OE1 GLU B 854 " pdb=" H GLU B 854 " model vdw 1.500 1.850 nonbonded pdb=" OE1 GLU B2043 " pdb=" H GLU B2043 " model vdw 1.515 1.850 ... (remaining 1847039 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 235 through 672 or (resid 673 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or resid 689 through 1696 or \ resid 1718 through 2612 or resid 3001 through 3004)) selection = (chain 'B' and (resid 235 through 672 or (resid 673 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or resid 689 through 2612 or \ resid 3001 through 3004)) selection = (chain 'C' and (resid 235 through 673 or (resid 689 and (name N or name CA or na \ me C or name O or name CB or name HA )) or resid 690 through 1037 or (resid 1043 \ and (name N or name CA or name C or name O or name CB or name OG or name HA or \ name HB2 or name HB3 or name HG )) or resid 1044 through 1696 or resid 1718 thro \ ugh 2612 or resid 3001 through 3004)) selection = (chain 'D' and (resid 235 through 672 or (resid 673 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or resid 689 through 1004 or \ (resid 1022 and (name N or name CA or name C or name O or name CB or name HA )) \ or resid 1023 through 1557 or (resid 1586 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or n \ ame CE3 or name CZ2 or name CZ3 or name CH2 or name HA or name HB2 or name HB3 o \ r name HD1 or name HE1 or name HE3 or name HZ2 or name HZ3 or name HH2)) or resi \ d 1587 through 1696 or resid 1718 through 2612 or resid 3001 through 3004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.340 Extract box with map and model: 29.810 Check model and map are aligned: 1.380 Set scattering table: 0.910 Process input model: 382.400 Find NCS groups from input model: 7.350 Set up NCS constraints: 0.540 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: 0.040 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 431.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 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 : 0.002 0.054 66269 Z= 0.145 Angle : 0.500 9.792 89581 Z= 0.272 Chirality : 0.035 0.291 10295 Planarity : 0.003 0.108 11334 Dihedral : 17.066 123.636 24999 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.43 % Favored : 98.55 % Rotamer: Outliers : 0.08 % Allowed : 14.75 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 3.35 (0.09), residues: 7908 helix: 2.98 (0.07), residues: 5472 sheet: 0.39 (0.24), residues: 435 loop : 0.47 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1127 HIS 0.015 0.001 HIS B1266 PHE 0.024 0.001 PHE A 761 TYR 0.022 0.001 TYR A 729 ARG 0.014 0.001 ARG C2131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1171 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1165 time to evaluate : 7.542 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 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 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 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 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 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 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 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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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: -0.1712 (ptp) cc_final: -0.2999 (mtt) REVERT: B 460 ASN cc_start: 0.5561 (m-40) cc_final: 0.4963 (t0) REVERT: B 768 MET cc_start: 0.5165 (ttt) cc_final: 0.4083 (tpp) REVERT: B 1272 TYR cc_start: 0.7323 (t80) cc_final: 0.7012 (t80) REVERT: B 1542 MET cc_start: 0.8133 (tmm) cc_final: 0.7443 (tmm) REVERT: B 1918 THR cc_start: 0.8129 (m) cc_final: 0.7903 (t) REVERT: B 2278 ILE cc_start: 0.7594 (mt) cc_final: 0.7153 (mt) REVERT: B 2345 LEU cc_start: 0.8817 (mt) cc_final: 0.8578 (mt) REVERT: C 708 VAL cc_start: 0.5747 (t) cc_final: 0.5535 (t) REVERT: C 1349 MET cc_start: -0.3776 (tpt) cc_final: -0.4144 (mtm) REVERT: C 1598 ILE cc_start: 0.7666 (mm) cc_final: 0.7361 (tt) REVERT: C 1869 ILE cc_start: 0.9014 (tp) cc_final: 0.8795 (tp) REVERT: C 2211 LEU cc_start: 0.9303 (mt) cc_final: 0.9095 (mm) REVERT: D 552 MET cc_start: 0.6925 (ttp) cc_final: 0.5935 (mtp) REVERT: D 618 PHE cc_start: 0.6181 (m-80) cc_final: 0.5776 (m-10) REVERT: D 1598 ILE cc_start: 0.7149 (mm) cc_final: 0.6914 (tp) outliers start: 6 outliers final: 1 residues processed: 1171 average time/residue: 1.6390 time to fit residues: 3148.7745 Evaluate side-chains 750 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 749 time to evaluate : 7.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2297 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 674 optimal weight: 9.9990 chunk 605 optimal weight: 0.9990 chunk 336 optimal weight: 20.0000 chunk 206 optimal weight: 50.0000 chunk 408 optimal weight: 40.0000 chunk 323 optimal weight: 7.9990 chunk 626 optimal weight: 30.0000 chunk 242 optimal weight: 40.0000 chunk 380 optimal weight: 6.9990 chunk 466 optimal weight: 5.9990 chunk 725 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 704 HIS ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS A1622 HIS A1636 GLN A1670 GLN ** A1896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2041 ASN B 573 HIS ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2179 HIS B2467 ASN C 551 HIS ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 HIS ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1266 HIS C1798 GLN C2179 HIS ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN D1086 GLN D1168 ASN D1288 HIS ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 GLN D1797 GLN D2035 GLN D2135 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 66269 Z= 0.370 Angle : 0.598 7.648 89581 Z= 0.327 Chirality : 0.037 0.195 10295 Planarity : 0.004 0.103 11334 Dihedral : 5.707 88.973 8898 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.80 % Favored : 98.18 % Rotamer: Outliers : 2.13 % Allowed : 15.76 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.58 (0.09), residues: 7908 helix: 2.36 (0.07), residues: 5549 sheet: 0.16 (0.23), residues: 442 loop : 0.21 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1127 HIS 0.008 0.001 HIS A2468 PHE 0.025 0.002 PHE D1092 TYR 0.019 0.002 TYR C2381 ARG 0.012 0.001 ARG D2524 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 819 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 664 time to evaluate : 7.837 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 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 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 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 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 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: -0.1364 (ptp) cc_final: -0.2911 (mtt) REVERT: A 739 MET cc_start: 0.5278 (mmm) cc_final: 0.4462 (mmm) REVERT: A 2166 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 703 HIS cc_start: 0.4840 (OUTLIER) cc_final: 0.2950 (m-70) REVERT: B 768 MET cc_start: 0.5308 (ttt) cc_final: 0.4121 (tpp) REVERT: B 1272 TYR cc_start: 0.7498 (t80) cc_final: 0.7179 (t80) REVERT: B 1542 MET cc_start: 0.8133 (tmm) cc_final: 0.7328 (tmm) REVERT: B 1992 LEU cc_start: 0.8302 (tp) cc_final: 0.8047 (tp) REVERT: B 2593 MET cc_start: 0.8154 (mmm) cc_final: 0.7660 (mmm) REVERT: C 1182 MET cc_start: 0.5946 (mtm) cc_final: 0.5382 (mtp) REVERT: C 1348 MET cc_start: 0.3564 (ppp) cc_final: 0.2927 (ppp) REVERT: D 552 MET cc_start: 0.7094 (ttp) cc_final: 0.6085 (mtp) REVERT: D 580 MET cc_start: 0.7187 (tmm) cc_final: 0.6911 (tmm) REVERT: D 618 PHE cc_start: 0.6103 (m-80) cc_final: 0.5586 (m-10) outliers start: 155 outliers final: 84 residues processed: 796 average time/residue: 1.5064 time to fit residues: 1982.5078 Evaluate side-chains 658 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 572 time to evaluate : 7.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1922 LEU Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 1964 SER Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2038 GLU Chi-restraints excluded: chain A residue 2118 GLU Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2594 ILE Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 1220 LYS Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1948 CYS Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2038 GLU Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1597 ASP Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1905 CYS Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2198 SER Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 987 ILE Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1079 PHE Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1498 VAL Chi-restraints excluded: chain D residue 1599 ILE Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 2034 LEU Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 403 optimal weight: 40.0000 chunk 225 optimal weight: 40.0000 chunk 603 optimal weight: 50.0000 chunk 494 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 726 optimal weight: 10.0000 chunk 785 optimal weight: 0.9990 chunk 647 optimal weight: 10.0000 chunk 720 optimal weight: 2.9990 chunk 247 optimal weight: 40.0000 chunk 583 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS ** A1896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2041 ASN A2129 GLN ** A2467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1065 HIS B1106 ASN B1193 GLN ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1965 ASN ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2579 ASN ** B2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1304 HIS ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1031 GLN ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1565 ASN D1871 GLN D1965 ASN D2592 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 66269 Z= 0.286 Angle : 0.521 8.373 89581 Z= 0.283 Chirality : 0.035 0.180 10295 Planarity : 0.003 0.080 11334 Dihedral : 5.144 84.201 8898 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 1.98 % Allowed : 15.91 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.56 (0.09), residues: 7908 helix: 2.38 (0.07), residues: 5518 sheet: 0.01 (0.23), residues: 447 loop : 0.17 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1127 HIS 0.015 0.001 HIS C 551 PHE 0.015 0.001 PHE D 994 TYR 0.017 0.001 TYR C2381 ARG 0.007 0.001 ARG D2524 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 737 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 593 time to evaluate : 7.646 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 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 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 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 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 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 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 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 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 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: A 581 MET cc_start: -0.1292 (ptp) cc_final: -0.2819 (mtt) REVERT: A 1269 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7883 (tp) REVERT: A 1285 HIS cc_start: 0.5996 (OUTLIER) cc_final: 0.5554 (p-80) REVERT: A 1349 MET cc_start: -0.2468 (ptt) cc_final: -0.2756 (ptt) REVERT: A 1870 MET cc_start: 0.6272 (tpt) cc_final: 0.5929 (tpt) REVERT: B 703 HIS cc_start: 0.5091 (OUTLIER) cc_final: 0.3153 (m-70) REVERT: B 739 MET cc_start: 0.2225 (mtm) cc_final: 0.1757 (mmm) REVERT: B 768 MET cc_start: 0.5310 (ttt) cc_final: 0.4208 (tpp) REVERT: B 1272 TYR cc_start: 0.7459 (t80) cc_final: 0.7107 (t80) REVERT: B 1348 MET cc_start: -0.1451 (OUTLIER) cc_final: -0.1721 (mpp) REVERT: B 1438 TRP cc_start: 0.2484 (m100) cc_final: 0.2258 (m100) REVERT: B 1542 MET cc_start: 0.8212 (tmm) cc_final: 0.7492 (tmm) REVERT: B 1992 LEU cc_start: 0.8259 (tp) cc_final: 0.8020 (tp) REVERT: B 2593 MET cc_start: 0.8122 (mmm) cc_final: 0.7679 (mmm) REVERT: C 551 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.8021 (t70) REVERT: C 1182 MET cc_start: 0.5925 (mtm) cc_final: 0.5356 (mtp) REVERT: C 1348 MET cc_start: 0.3634 (ppp) cc_final: 0.3003 (ppp) REVERT: D 552 MET cc_start: 0.7175 (ttp) cc_final: 0.6184 (mtp) REVERT: D 581 MET cc_start: 0.7407 (mtp) cc_final: 0.6810 (mpp) outliers start: 144 outliers final: 101 residues processed: 711 average time/residue: 1.4458 time to fit residues: 1696.1961 Evaluate side-chains 646 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 540 time to evaluate : 7.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1793 MET Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2038 GLU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1348 MET Chi-restraints excluded: chain B residue 1668 THR Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2038 GLU Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2272 SER Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1299 TYR Chi-restraints excluded: chain C residue 1304 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1905 CYS Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2170 ASP Chi-restraints excluded: chain C residue 2198 SER Chi-restraints excluded: chain C residue 2269 ILE Chi-restraints excluded: chain C residue 2273 ILE Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2467 ASN Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1498 VAL Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2299 SER Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 718 optimal weight: 7.9990 chunk 546 optimal weight: 6.9990 chunk 377 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 488 optimal weight: 20.0000 chunk 729 optimal weight: 8.9990 chunk 772 optimal weight: 3.9990 chunk 381 optimal weight: 1.9990 chunk 691 optimal weight: 30.0000 chunk 208 optimal weight: 40.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2041 ASN ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1288 HIS ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1590 ASN D1696 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 66269 Z= 0.255 Angle : 0.499 6.946 89581 Z= 0.271 Chirality : 0.034 0.166 10295 Planarity : 0.003 0.073 11334 Dihedral : 4.987 85.507 8898 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.82 % Rotamer: Outliers : 2.12 % Allowed : 15.87 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.58 (0.09), residues: 7908 helix: 2.39 (0.07), residues: 5521 sheet: -0.04 (0.23), residues: 443 loop : 0.18 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1127 HIS 0.030 0.001 HIS A1304 PHE 0.017 0.001 PHE B1444 TYR 0.019 0.001 TYR D1272 ARG 0.008 0.000 ARG A2062 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 711 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 557 time to evaluate : 7.662 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 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 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 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 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 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 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 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 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 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: A 581 MET cc_start: -0.1367 (ptp) cc_final: -0.2759 (mtt) REVERT: A 1285 HIS cc_start: 0.5984 (OUTLIER) cc_final: 0.5577 (p-80) REVERT: A 1349 MET cc_start: -0.2567 (ptt) cc_final: -0.2823 (ptt) REVERT: A 1870 MET cc_start: 0.6323 (tpt) cc_final: 0.6026 (tpt) REVERT: B 703 HIS cc_start: 0.5229 (OUTLIER) cc_final: 0.3226 (m-70) REVERT: B 739 MET cc_start: 0.2365 (mtm) cc_final: 0.1902 (mmm) REVERT: B 768 MET cc_start: 0.5354 (ttt) cc_final: 0.4570 (tpp) REVERT: B 1272 TYR cc_start: 0.7495 (t80) cc_final: 0.7117 (t80) REVERT: B 1542 MET cc_start: 0.8268 (tmm) cc_final: 0.7609 (tmm) REVERT: B 1655 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7533 (tmm) REVERT: B 1992 LEU cc_start: 0.8280 (tp) cc_final: 0.8038 (tp) REVERT: C 1182 MET cc_start: 0.6121 (mtm) cc_final: 0.5593 (mtp) REVERT: C 1348 MET cc_start: 0.3765 (OUTLIER) cc_final: 0.3137 (ppp) REVERT: D 581 MET cc_start: 0.7459 (mtp) cc_final: 0.6947 (mpp) outliers start: 154 outliers final: 110 residues processed: 683 average time/residue: 1.4841 time to fit residues: 1686.7853 Evaluate side-chains 639 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 525 time to evaluate : 7.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1897 ASN Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2038 GLU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 861 PHE Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1655 MET Chi-restraints excluded: chain B residue 1668 THR Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2038 GLU Chi-restraints excluded: chain B residue 2118 GLU Chi-restraints excluded: chain B residue 2127 VAL Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2273 ILE Chi-restraints excluded: chain B residue 2285 LEU Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1227 TYR Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1348 MET Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1597 ASP Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1905 CYS Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2170 ASP Chi-restraints excluded: chain C residue 2273 ILE Chi-restraints excluded: chain C residue 2281 THR Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2467 ASN Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 671 ARG Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1498 VAL Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 2034 LEU Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 643 optimal weight: 1.9990 chunk 438 optimal weight: 8.9990 chunk 11 optimal weight: 40.0000 chunk 575 optimal weight: 1.9990 chunk 318 optimal weight: 30.0000 chunk 659 optimal weight: 9.9990 chunk 533 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 394 optimal weight: 5.9990 chunk 693 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1684 ASN ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2041 ASN ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1168 ASN ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 GLN ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2592 GLN ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1193 GLN ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1995 ASN D2123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 66269 Z= 0.238 Angle : 0.486 7.417 89581 Z= 0.263 Chirality : 0.034 0.162 10295 Planarity : 0.003 0.063 11334 Dihedral : 4.946 83.614 8898 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 2.08 % Allowed : 15.93 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.66 (0.09), residues: 7908 helix: 2.46 (0.07), residues: 5517 sheet: -0.17 (0.23), residues: 457 loop : 0.25 (0.15), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1127 HIS 0.014 0.001 HIS A1547 PHE 0.014 0.001 PHE D1910 TYR 0.022 0.001 TYR C2589 ARG 0.007 0.000 ARG D2524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 702 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 551 time to evaluate : 7.687 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 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 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 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: -0.1454 (ptp) cc_final: -0.2746 (mtt) REVERT: A 1023 MET cc_start: -0.0223 (mmm) cc_final: -0.0522 (mmm) REVERT: A 1285 HIS cc_start: 0.5980 (OUTLIER) cc_final: 0.5578 (p-80) REVERT: A 1349 MET cc_start: -0.2616 (ptt) cc_final: -0.2854 (ptt) REVERT: A 1870 MET cc_start: 0.6348 (tpt) cc_final: 0.4927 (tpt) REVERT: B 416 MET cc_start: 0.2879 (tpt) cc_final: 0.2647 (tpt) REVERT: B 703 HIS cc_start: 0.5247 (OUTLIER) cc_final: 0.3258 (m-70) REVERT: B 739 MET cc_start: 0.2387 (mtm) cc_final: 0.1666 (tpp) REVERT: B 768 MET cc_start: 0.5919 (ttt) cc_final: 0.4573 (tpp) REVERT: B 1348 MET cc_start: -0.1640 (mpp) cc_final: -0.1916 (mpp) REVERT: B 1542 MET cc_start: 0.8265 (tmm) cc_final: 0.7639 (tmm) REVERT: B 1655 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7534 (tmm) REVERT: B 1992 LEU cc_start: 0.8243 (tp) cc_final: 0.7993 (tp) REVERT: C 581 MET cc_start: 0.7362 (mmt) cc_final: 0.6789 (mmt) REVERT: C 1115 ASP cc_start: 0.9107 (t0) cc_final: 0.8700 (m-30) REVERT: C 1348 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3294 (ppp) REVERT: C 1349 MET cc_start: -0.5289 (ttp) cc_final: -0.5622 (ttp) REVERT: C 2203 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9252 (tp) REVERT: D 581 MET cc_start: 0.7425 (mtp) cc_final: 0.6940 (mpp) outliers start: 151 outliers final: 119 residues processed: 671 average time/residue: 1.4172 time to fit residues: 1579.9985 Evaluate side-chains 652 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 528 time to evaluate : 7.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1897 ASN Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2038 GLU Chi-restraints excluded: chain A residue 2068 GLN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 861 PHE Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1443 ASN Chi-restraints excluded: chain B residue 1529 LEU Chi-restraints excluded: chain B residue 1655 MET Chi-restraints excluded: chain B residue 1668 THR Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2038 GLU Chi-restraints excluded: chain B residue 2127 VAL Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2285 LEU Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1227 TYR Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1348 MET Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1597 ASP Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2170 ASP Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2281 THR Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2467 ASN Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1259 LEU Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1691 LEU Chi-restraints excluded: chain D residue 1785 PHE Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1925 LEU Chi-restraints excluded: chain D residue 2034 LEU Chi-restraints excluded: chain D residue 2048 GLU Chi-restraints excluded: chain D residue 2118 GLU Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 259 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 453 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 773 optimal weight: 9.9990 chunk 641 optimal weight: 20.0000 chunk 357 optimal weight: 0.9990 chunk 64 optimal weight: 30.0000 chunk 255 optimal weight: 20.0000 chunk 405 optimal weight: 8.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 ASN ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 66269 Z= 0.269 Angle : 0.500 7.639 89581 Z= 0.273 Chirality : 0.034 0.172 10295 Planarity : 0.003 0.062 11334 Dihedral : 4.954 82.246 8898 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 2.32 % Allowed : 15.93 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.54 (0.09), residues: 7908 helix: 2.36 (0.07), residues: 5518 sheet: -0.21 (0.23), residues: 453 loop : 0.22 (0.15), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1127 HIS 0.007 0.001 HIS B2558 PHE 0.017 0.001 PHE C 878 TYR 0.018 0.001 TYR C2381 ARG 0.011 0.000 ARG D 730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 699 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 530 time to evaluate : 7.776 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 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 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 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 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 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 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 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 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 REVERT: A 581 MET cc_start: -0.1548 (ptp) cc_final: -0.2717 (mtt) REVERT: A 1285 HIS cc_start: 0.5939 (OUTLIER) cc_final: 0.5545 (p-80) REVERT: A 1349 MET cc_start: -0.2478 (ptt) cc_final: -0.2720 (ptt) REVERT: B 416 MET cc_start: 0.2926 (tpt) cc_final: 0.2701 (tpt) REVERT: B 703 HIS cc_start: 0.5079 (OUTLIER) cc_final: 0.3080 (m-70) REVERT: B 739 MET cc_start: 0.2510 (mtm) cc_final: 0.2067 (mmm) REVERT: B 768 MET cc_start: 0.6015 (ttt) cc_final: 0.4686 (tpp) REVERT: B 1542 MET cc_start: 0.8244 (tmm) cc_final: 0.7639 (tmm) REVERT: B 1655 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7541 (tmm) REVERT: B 1992 LEU cc_start: 0.8267 (tp) cc_final: 0.8005 (tp) REVERT: B 2398 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: B 2593 MET cc_start: 0.8096 (mmm) cc_final: 0.7702 (mmm) REVERT: C 1115 ASP cc_start: 0.9131 (t0) cc_final: 0.8764 (m-30) REVERT: C 1348 MET cc_start: 0.3979 (OUTLIER) cc_final: 0.3380 (ppp) REVERT: C 2318 MET cc_start: 0.8654 (mmm) cc_final: 0.8439 (tpp) REVERT: D 581 MET cc_start: 0.7413 (mtp) cc_final: 0.6898 (mpp) REVERT: D 1080 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6582 (tptp) REVERT: D 2314 MET cc_start: 0.8789 (mtm) cc_final: 0.8547 (mtm) outliers start: 169 outliers final: 143 residues processed: 667 average time/residue: 1.4470 time to fit residues: 1603.9249 Evaluate side-chains 652 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 503 time to evaluate : 7.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1643 PHE Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 1897 ASN Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2038 GLU Chi-restraints excluded: chain A residue 2068 GLN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 861 PHE Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1655 MET Chi-restraints excluded: chain B residue 1668 THR Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2038 GLU Chi-restraints excluded: chain B residue 2118 GLU Chi-restraints excluded: chain B residue 2127 VAL Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2272 SER Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2398 GLU Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 978 ILE Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1227 TYR Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1348 MET Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1597 ASP Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2206 SER Chi-restraints excluded: chain C residue 2269 ILE Chi-restraints excluded: chain C residue 2273 ILE Chi-restraints excluded: chain C residue 2281 THR Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2467 ASN Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1080 LYS Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1098 LEU Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1112 SER Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1259 LEU Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1498 VAL Chi-restraints excluded: chain D residue 1599 ILE Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1619 ASP Chi-restraints excluded: chain D residue 1691 LEU Chi-restraints excluded: chain D residue 1752 GLU Chi-restraints excluded: chain D residue 1785 PHE Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1925 LEU Chi-restraints excluded: chain D residue 1942 GLU Chi-restraints excluded: chain D residue 2034 LEU Chi-restraints excluded: chain D residue 2048 GLU Chi-restraints excluded: chain D residue 2118 GLU Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2191 MET Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 745 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 440 optimal weight: 20.0000 chunk 564 optimal weight: 1.9990 chunk 437 optimal weight: 6.9990 chunk 650 optimal weight: 20.0000 chunk 431 optimal weight: 5.9990 chunk 770 optimal weight: 3.9990 chunk 481 optimal weight: 8.9990 chunk 469 optimal weight: 2.9990 chunk 355 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1939 GLN ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2041 ASN ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 ASN ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2468 HIS ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 66269 Z= 0.193 Angle : 0.471 7.361 89581 Z= 0.251 Chirality : 0.034 0.144 10295 Planarity : 0.003 0.052 11334 Dihedral : 4.800 82.538 8897 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 2.05 % Allowed : 16.46 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.84 (0.10), residues: 7908 helix: 2.58 (0.07), residues: 5504 sheet: -0.21 (0.23), residues: 453 loop : 0.40 (0.15), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1127 HIS 0.014 0.001 HIS A1304 PHE 0.026 0.001 PHE B1444 TYR 0.015 0.001 TYR A 989 ARG 0.007 0.000 ARG D 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 681 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 532 time to evaluate : 7.672 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 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 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 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 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 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 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 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 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: A 581 MET cc_start: -0.1568 (ptp) cc_final: -0.2645 (mtt) REVERT: A 1285 HIS cc_start: 0.5935 (OUTLIER) cc_final: 0.5531 (p-80) REVERT: A 1349 MET cc_start: -0.2553 (ptt) cc_final: -0.2812 (ptt) REVERT: A 2166 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 2565 MET cc_start: 0.7450 (ptm) cc_final: 0.7183 (ptm) REVERT: B 416 MET cc_start: 0.2912 (tpt) cc_final: 0.2698 (tpt) REVERT: B 768 MET cc_start: 0.6145 (ttt) cc_final: 0.4779 (tpp) REVERT: B 1655 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7540 (tmm) REVERT: B 1992 LEU cc_start: 0.8241 (tp) cc_final: 0.7975 (tp) REVERT: C 509 MET cc_start: 0.2183 (mmm) cc_final: 0.1962 (mmm) REVERT: C 1115 ASP cc_start: 0.9132 (t0) cc_final: 0.8763 (m-30) REVERT: C 1348 MET cc_start: 0.4025 (OUTLIER) cc_final: 0.3433 (ppp) REVERT: C 2203 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9187 (tp) REVERT: D 581 MET cc_start: 0.7359 (mtp) cc_final: 0.6985 (mpp) REVERT: D 2314 MET cc_start: 0.8755 (mtm) cc_final: 0.8510 (mtm) outliers start: 149 outliers final: 121 residues processed: 650 average time/residue: 1.6126 time to fit residues: 1765.3916 Evaluate side-chains 637 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 511 time to evaluate : 7.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1643 PHE Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1897 ASN Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2068 GLN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 861 PHE Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1529 LEU Chi-restraints excluded: chain B residue 1655 MET Chi-restraints excluded: chain B residue 1668 THR Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2127 VAL Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 978 ILE Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1227 TYR Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1348 MET Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1597 ASP Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2206 SER Chi-restraints excluded: chain C residue 2273 ILE Chi-restraints excluded: chain C residue 2281 THR Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2314 MET Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2528 GLN Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 813 LYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1259 LEU Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1599 ILE Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1691 LEU Chi-restraints excluded: chain D residue 1752 GLU Chi-restraints excluded: chain D residue 1785 PHE Chi-restraints excluded: chain D residue 1942 GLU Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2034 LEU Chi-restraints excluded: chain D residue 2118 GLU Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2321 LEU Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 476 optimal weight: 10.0000 chunk 307 optimal weight: 50.0000 chunk 459 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 489 optimal weight: 30.0000 chunk 524 optimal weight: 6.9990 chunk 380 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 605 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 710 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1318 GLN B1365 HIS ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1230 GLN ** C1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 ASN ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 GLN ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1076 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1798 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 66269 Z= 0.392 Angle : 0.581 8.869 89581 Z= 0.324 Chirality : 0.036 0.221 10295 Planarity : 0.004 0.062 11334 Dihedral : 5.151 86.833 8897 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 2.41 % Allowed : 16.55 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 1.97 (0.09), residues: 7908 helix: 1.94 (0.07), residues: 5530 sheet: -0.59 (0.23), residues: 442 loop : 0.02 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1127 HIS 0.025 0.001 HIS A1547 PHE 0.018 0.002 PHE C2539 TYR 0.024 0.002 TYR C2381 ARG 0.008 0.001 ARG D2524 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 656 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 481 time to evaluate : 7.608 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 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: -0.1557 (ptp) cc_final: -0.2580 (mtt) REVERT: A 1285 HIS cc_start: 0.5918 (OUTLIER) cc_final: 0.5555 (p-80) REVERT: A 1349 MET cc_start: -0.2504 (ptt) cc_final: -0.2759 (ptt) REVERT: A 2181 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: A 2524 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7965 (ttm-80) REVERT: B 416 MET cc_start: 0.2976 (tpt) cc_final: 0.2771 (tpt) REVERT: B 703 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.3265 (m-70) REVERT: B 739 MET cc_start: 0.2530 (mtm) cc_final: 0.1947 (tpp) REVERT: B 768 MET cc_start: 0.6439 (ttt) cc_final: 0.5121 (tpp) REVERT: B 1023 MET cc_start: 0.1255 (mtt) cc_final: 0.0190 (mtp) REVERT: B 1348 MET cc_start: -0.0935 (mpp) cc_final: -0.1366 (mpp) REVERT: B 1542 MET cc_start: 0.8270 (tmm) cc_final: 0.7729 (tmm) REVERT: B 1655 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7580 (tmm) REVERT: B 2398 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: B 2593 MET cc_start: 0.8134 (mmm) cc_final: 0.7701 (mmm) REVERT: C 552 MET cc_start: 0.5992 (ttt) cc_final: 0.5743 (mtp) REVERT: C 1348 MET cc_start: 0.4246 (OUTLIER) cc_final: 0.3625 (ppp) REVERT: C 1349 MET cc_start: -0.4800 (ttp) cc_final: -0.5287 (ttp) REVERT: C 2593 MET cc_start: 0.8264 (tpp) cc_final: 0.8018 (mpp) REVERT: D 552 MET cc_start: 0.7301 (ttp) cc_final: 0.6875 (tmm) REVERT: D 618 PHE cc_start: 0.5920 (m-80) cc_final: 0.5710 (m-10) REVERT: D 2329 THR cc_start: 0.9415 (m) cc_final: 0.9204 (p) outliers start: 175 outliers final: 146 residues processed: 617 average time/residue: 1.4484 time to fit residues: 1499.4942 Evaluate side-chains 616 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 463 time to evaluate : 7.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1643 PHE Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1887 ASP Chi-restraints excluded: chain A residue 1897 ASN Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2048 GLU Chi-restraints excluded: chain A residue 2068 GLN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2524 ARG Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 861 PHE Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1529 LEU Chi-restraints excluded: chain B residue 1655 MET Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2038 GLU Chi-restraints excluded: chain B residue 2127 VAL Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2272 SER Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2398 GLU Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 978 ILE Chi-restraints excluded: chain C residue 1077 LEU Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1227 TYR Chi-restraints excluded: chain C residue 1288 HIS Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1348 MET Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1597 ASP Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1905 CYS Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2273 ILE Chi-restraints excluded: chain C residue 2281 THR Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2314 MET Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2467 ASN Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 813 LYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1098 LEU Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1250 LEU Chi-restraints excluded: chain D residue 1259 LEU Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1599 ILE Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1619 ASP Chi-restraints excluded: chain D residue 1691 LEU Chi-restraints excluded: chain D residue 1752 GLU Chi-restraints excluded: chain D residue 1785 PHE Chi-restraints excluded: chain D residue 1907 THR Chi-restraints excluded: chain D residue 1942 GLU Chi-restraints excluded: chain D residue 2118 GLU Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2198 SER Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2532 GLU Chi-restraints excluded: chain D residue 2592 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 700 optimal weight: 10.0000 chunk 737 optimal weight: 2.9990 chunk 673 optimal weight: 1.9990 chunk 717 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 563 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 648 optimal weight: 0.2980 chunk 678 optimal weight: 20.0000 chunk 715 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 GLN ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2035 GLN ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1211 GLN ** C1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2119 ASN ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2179 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 66269 Z= 0.202 Angle : 0.492 8.559 89581 Z= 0.262 Chirality : 0.034 0.188 10295 Planarity : 0.003 0.053 11334 Dihedral : 4.932 89.570 8897 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 17.14 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.47 (0.09), residues: 7908 helix: 2.31 (0.07), residues: 5520 sheet: -0.48 (0.24), residues: 439 loop : 0.25 (0.15), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1127 HIS 0.015 0.001 HIS A1547 PHE 0.014 0.001 PHE C1785 TYR 0.015 0.001 TYR B1067 ARG 0.010 0.000 ARG A1226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 644 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 500 time to evaluate : 7.576 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 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: -0.1607 (ptp) cc_final: -0.2492 (mtt) REVERT: A 1793 MET cc_start: 0.6503 (mmm) cc_final: 0.6142 (mmm) REVERT: A 2166 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8440 (p) REVERT: A 2201 MET cc_start: 0.8624 (tpp) cc_final: 0.8358 (tpp) REVERT: B 416 MET cc_start: 0.2970 (tpt) cc_final: 0.2768 (tpt) REVERT: B 460 ASN cc_start: 0.4891 (m-40) cc_final: 0.3823 (t0) REVERT: B 739 MET cc_start: 0.2571 (mtm) cc_final: 0.1978 (tpp) REVERT: B 768 MET cc_start: 0.6440 (ttt) cc_final: 0.5107 (tpp) REVERT: B 1023 MET cc_start: 0.1168 (mtt) cc_final: 0.0201 (mtp) REVERT: B 1348 MET cc_start: -0.0987 (mpp) cc_final: -0.1368 (mpp) REVERT: B 1655 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7552 (tmm) REVERT: C 552 MET cc_start: 0.5965 (ttt) cc_final: 0.5728 (mtp) REVERT: C 1182 MET cc_start: 0.6554 (ttp) cc_final: 0.6270 (ttt) REVERT: C 1236 CYS cc_start: 0.5772 (OUTLIER) cc_final: 0.5082 (p) REVERT: C 1348 MET cc_start: 0.4276 (OUTLIER) cc_final: 0.3678 (ppp) REVERT: C 1349 MET cc_start: -0.4911 (ttp) cc_final: -0.5166 (ttp) REVERT: C 2593 MET cc_start: 0.8149 (tpp) cc_final: 0.7934 (mpp) REVERT: D 552 MET cc_start: 0.7296 (ttp) cc_final: 0.6873 (tmm) REVERT: D 581 MET cc_start: 0.7494 (mtp) cc_final: 0.6950 (mpp) REVERT: D 2314 MET cc_start: 0.8714 (mtm) cc_final: 0.8464 (mtm) outliers start: 144 outliers final: 125 residues processed: 611 average time/residue: 1.5351 time to fit residues: 1588.0457 Evaluate side-chains 609 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 480 time to evaluate : 7.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain A residue 1643 PHE Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1897 ASN Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2068 GLN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2264 LEU Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 861 PHE Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1529 LEU Chi-restraints excluded: chain B residue 1551 MET Chi-restraints excluded: chain B residue 1655 MET Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2127 VAL Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2272 SER Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 978 ILE Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1227 TYR Chi-restraints excluded: chain C residue 1236 CYS Chi-restraints excluded: chain C residue 1288 HIS Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1348 MET Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2273 ILE Chi-restraints excluded: chain C residue 2281 THR Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2467 ASN Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 813 LYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1098 LEU Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1250 LEU Chi-restraints excluded: chain D residue 1279 SER Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1599 ILE Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1691 LEU Chi-restraints excluded: chain D residue 1752 GLU Chi-restraints excluded: chain D residue 1785 PHE Chi-restraints excluded: chain D residue 1942 GLU Chi-restraints excluded: chain D residue 2118 GLU Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2198 SER Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 471 optimal weight: 0.9990 chunk 758 optimal weight: 5.9990 chunk 463 optimal weight: 9.9990 chunk 359 optimal weight: 5.9990 chunk 527 optimal weight: 4.9990 chunk 796 optimal weight: 0.2980 chunk 732 optimal weight: 8.9990 chunk 633 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 489 optimal weight: 20.0000 chunk 388 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1168 ASN A1170 GLN ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 66269 Z= 0.207 Angle : 0.553 59.200 89581 Z= 0.304 Chirality : 0.034 0.172 10295 Planarity : 0.003 0.053 11334 Dihedral : 4.928 89.576 8897 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.84 % Allowed : 17.32 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.50 (0.09), residues: 7908 helix: 2.33 (0.07), residues: 5520 sheet: -0.48 (0.24), residues: 439 loop : 0.26 (0.15), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B2566 HIS 0.066 0.001 HIS D 783 PHE 0.028 0.001 PHE D 618 TYR 0.090 0.001 TYR A1928 ARG 0.007 0.000 ARG D2524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15816 Ramachandran restraints generated. 7908 Oldfield, 0 Emsley, 7908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 616 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 482 time to evaluate : 7.717 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 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 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 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 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 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 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 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: A 581 MET cc_start: -0.1611 (ptp) cc_final: -0.2494 (mtt) REVERT: A 2166 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8435 (p) REVERT: A 2181 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: A 2201 MET cc_start: 0.8619 (tpp) cc_final: 0.8350 (tpp) REVERT: B 416 MET cc_start: 0.2970 (tpt) cc_final: 0.2768 (tpt) REVERT: B 460 ASN cc_start: 0.4889 (m-40) cc_final: 0.3823 (t0) REVERT: B 739 MET cc_start: 0.2570 (mtm) cc_final: 0.1974 (tpp) REVERT: B 768 MET cc_start: 0.6438 (ttt) cc_final: 0.5105 (tpp) REVERT: B 1023 MET cc_start: 0.1166 (mtt) cc_final: 0.0200 (mtp) REVERT: B 1348 MET cc_start: -0.1006 (mpp) cc_final: -0.1352 (mpp) REVERT: B 1655 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7551 (tmm) REVERT: C 552 MET cc_start: 0.5963 (ttt) cc_final: 0.5727 (mtp) REVERT: C 1182 MET cc_start: 0.6550 (ttp) cc_final: 0.6265 (ttt) REVERT: C 1236 CYS cc_start: 0.5773 (OUTLIER) cc_final: 0.5082 (p) REVERT: C 1348 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.3678 (ppp) REVERT: C 1349 MET cc_start: -0.4915 (ttp) cc_final: -0.5165 (ttp) REVERT: C 2593 MET cc_start: 0.8138 (tpp) cc_final: 0.7924 (mpp) REVERT: D 552 MET cc_start: 0.7293 (ttp) cc_final: 0.6871 (tmm) REVERT: D 581 MET cc_start: 0.7502 (mtp) cc_final: 0.6966 (mpp) REVERT: D 2314 MET cc_start: 0.8712 (mtm) cc_final: 0.8461 (mtm) outliers start: 134 outliers final: 125 residues processed: 587 average time/residue: 1.5185 time to fit residues: 1507.5297 Evaluate side-chains 609 residues out of total 7291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 479 time to evaluate : 9.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1214 TYR Chi-restraints excluded: chain A residue 1375 CYS Chi-restraints excluded: chain A residue 1643 PHE Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1897 ASN Chi-restraints excluded: chain A residue 1915 CYS Chi-restraints excluded: chain A residue 1958 CYS Chi-restraints excluded: chain A residue 2014 GLU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2068 GLN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2268 LEU Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2368 SER Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2533 ILE Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 861 PHE Chi-restraints excluded: chain B residue 1072 SER Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1529 LEU Chi-restraints excluded: chain B residue 1551 MET Chi-restraints excluded: chain B residue 1655 MET Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2127 VAL Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2272 SER Chi-restraints excluded: chain B residue 2289 ASN Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2582 ASP Chi-restraints excluded: chain C residue 551 HIS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 864 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 978 ILE Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1227 TYR Chi-restraints excluded: chain C residue 1236 CYS Chi-restraints excluded: chain C residue 1288 HIS Chi-restraints excluded: chain C residue 1296 HIS Chi-restraints excluded: chain C residue 1315 LYS Chi-restraints excluded: chain C residue 1348 MET Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1927 LEU Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2273 ILE Chi-restraints excluded: chain C residue 2281 THR Chi-restraints excluded: chain C residue 2288 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 HIS Chi-restraints excluded: chain D residue 813 LYS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1250 LEU Chi-restraints excluded: chain D residue 1279 SER Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1314 VAL Chi-restraints excluded: chain D residue 1390 LEU Chi-restraints excluded: chain D residue 1594 LYS Chi-restraints excluded: chain D residue 1599 ILE Chi-restraints excluded: chain D residue 1604 GLU Chi-restraints excluded: chain D residue 1691 LEU Chi-restraints excluded: chain D residue 1752 GLU Chi-restraints excluded: chain D residue 1785 PHE Chi-restraints excluded: chain D residue 1942 GLU Chi-restraints excluded: chain D residue 2118 GLU Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2198 SER Chi-restraints excluded: chain D residue 2211 LEU Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2321 LEU Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 503 optimal weight: 5.9990 chunk 675 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 584 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 634 optimal weight: 20.0000 chunk 265 optimal weight: 50.0000 chunk 651 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 GLN ** A1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.124788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.098166 restraints weight = 1366549.943| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 7.09 r_work: 0.3320 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 66269 Z= 0.207 Angle : 0.553 59.200 89581 Z= 0.304 Chirality : 0.034 0.172 10295 Planarity : 0.003 0.053 11334 Dihedral : 4.928 89.576 8897 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.79 % Allowed : 17.35 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % 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: 2.50 (0.09), residues: 7908 helix: 2.33 (0.07), residues: 5520 sheet: -0.48 (0.24), residues: 439 loop : 0.26 (0.15), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B2566 HIS 0.066 0.001 HIS D 783 PHE 0.028 0.001 PHE D 618 TYR 0.090 0.001 TYR A1928 ARG 0.007 0.000 ARG D2524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34257.82 seconds wall clock time: 588 minutes 49.19 seconds (35329.19 seconds total)