Starting phenix.real_space_refine on Tue Feb 13 23:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzo_26213/02_2024/7tzo_26213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzo_26213/02_2024/7tzo_26213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzo_26213/02_2024/7tzo_26213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzo_26213/02_2024/7tzo_26213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzo_26213/02_2024/7tzo_26213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tzo_26213/02_2024/7tzo_26213.pdb" } resolution = 3.28 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= 0.026 sd= 1.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 334 5.16 5 C 36166 2.51 5 N 10168 2.21 5 O 10449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A PHE 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A GLU 1040": "OE1" <-> "OE2" Residue "A PHE 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1109": "OD1" <-> "OD2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A ASP 1175": "OD1" <-> "OD2" Residue "A PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1201": "NH1" <-> "NH2" Residue "A ARG 1215": "NH1" <-> "NH2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1238": "NH1" <-> "NH2" Residue "A ASP 1278": "OD1" <-> "OD2" Residue "A ASP 1279": "OD1" <-> "OD2" Residue "A ASP 1294": "OD1" <-> "OD2" Residue "A GLU 1331": "OE1" <-> "OE2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A ASP 1376": "OD1" <-> "OD2" Residue "A ASP 1377": "OD1" <-> "OD2" Residue "A TYR 1399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1403": "OE1" <-> "OE2" Residue "A GLU 1427": "OE1" <-> "OE2" Residue "A GLU 1451": "OE1" <-> "OE2" Residue "A ASP 1464": "OD1" <-> "OD2" Residue "A GLU 1489": "OE1" <-> "OE2" Residue "A GLU 1507": "OE1" <-> "OE2" Residue "A PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1555": "OD1" <-> "OD2" Residue "A ASP 1565": "OD1" <-> "OD2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "A GLU 1613": "OE1" <-> "OE2" Residue "A ARG 1683": "NH1" <-> "NH2" Residue "A TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1905": "NH1" <-> "NH2" Residue "A PHE 1911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1955": "NH1" <-> "NH2" Residue "A TYR 1967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2014": "OE1" <-> "OE2" Residue "A GLU 2015": "OE1" <-> "OE2" Residue "A PHE 2070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2086": "NH1" <-> "NH2" Residue "A ASP 2102": "OD1" <-> "OD2" Residue "A ARG 2134": "NH1" <-> "NH2" Residue "A GLU 2137": "OE1" <-> "OE2" Residue "A ASP 2244": "OD1" <-> "OD2" Residue "A ASP 2252": "OD1" <-> "OD2" Residue "A GLU 2255": "OE1" <-> "OE2" Residue "A ASP 2297": "OD1" <-> "OD2" Residue "A ASP 2315": "OD1" <-> "OD2" Residue "A ASP 2360": "OD1" <-> "OD2" Residue "A GLU 2369": "OE1" <-> "OE2" Residue "A GLU 2419": "OE1" <-> "OE2" Residue "A ASP 2424": "OD1" <-> "OD2" Residue "A ASP 2433": "OD1" <-> "OD2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 866": "OE1" <-> "OE2" Residue "B TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 933": "OE1" <-> "OE2" Residue "B ASP 961": "OD1" <-> "OD2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ASP 1109": "OD1" <-> "OD2" Residue "B PHE 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1141": "NH1" <-> "NH2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1150": "OD1" <-> "OD2" Residue "B ASP 1175": "OD1" <-> "OD2" Residue "B ARG 1215": "NH1" <-> "NH2" Residue "B ARG 1238": "NH1" <-> "NH2" Residue "B ASP 1279": "OD1" <-> "OD2" Residue "B ASP 1377": "OD1" <-> "OD2" Residue "B GLU 1427": "OE1" <-> "OE2" Residue "B ASP 1464": "OD1" <-> "OD2" Residue "B ASP 1468": "OD1" <-> "OD2" Residue "B ASP 1555": "OD1" <-> "OD2" Residue "B GLU 1574": "OE1" <-> "OE2" Residue "B GLU 1631": "OE1" <-> "OE2" Residue "B ARG 1683": "NH1" <-> "NH2" Residue "B TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1905": "NH1" <-> "NH2" Residue "B ASP 1947": "OD1" <-> "OD2" Residue "B ARG 1955": "NH1" <-> "NH2" Residue "B GLU 2015": "OE1" <-> "OE2" Residue "B PHE 2070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2086": "NH1" <-> "NH2" Residue "B ASP 2102": "OD1" <-> "OD2" Residue "B TYR 2105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2134": "NH1" <-> "NH2" Residue "B GLU 2181": "OE1" <-> "OE2" Residue "B PHE 2182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2244": "OD1" <-> "OD2" Residue "B ASP 2252": "OD1" <-> "OD2" Residue "B PHE 2362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2405": "OE1" <-> "OE2" Residue "B PHE 2421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2433": "OD1" <-> "OD2" Residue "B GLU 2526": "OE1" <-> "OE2" Residue "B PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E ARG 205": "NH1" <-> "NH2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ASP 360": "OD1" <-> "OD2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 495": "OD1" <-> "OD2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "E ARG 563": "NH1" <-> "NH2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "E TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 624": "OE1" <-> "OE2" Residue "E GLU 677": "OE1" <-> "OE2" Residue "E ARG 709": "NH1" <-> "NH2" Residue "E ARG 737": "NH1" <-> "NH2" Residue "E PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 841": "OD1" <-> "OD2" Residue "E TYR 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 960": "OE1" <-> "OE2" Residue "E ASP 1517": "OD1" <-> "OD2" Residue "E ASP 1518": "OD1" <-> "OD2" Residue "E PHE 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1666": "NH1" <-> "NH2" Residue "E PHE 1682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F ARG 205": "NH1" <-> "NH2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ASP 360": "OD1" <-> "OD2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F ASP 495": "OD1" <-> "OD2" Residue "F GLU 545": "OE1" <-> "OE2" Residue "F ARG 563": "NH1" <-> "NH2" Residue "F ARG 576": "NH1" <-> "NH2" Residue "F TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 624": "OE1" <-> "OE2" Residue "F GLU 677": "OE1" <-> "OE2" Residue "F ARG 709": "NH1" <-> "NH2" Residue "F ARG 737": "NH1" <-> "NH2" Residue "F PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 841": "OD1" <-> "OD2" Residue "F TYR 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 960": "OE1" <-> "OE2" Residue "F ASP 1517": "OD1" <-> "OD2" Residue "F ASP 1518": "OD1" <-> "OD2" Residue "F PHE 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1666": "NH1" <-> "NH2" Residue "F PHE 1682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 83": "NH1" <-> "NH2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 83": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 57117 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2184, 16337 Classifications: {'peptide': 2184} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 86, 'TRANS': 2097} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1316 Unresolved non-hydrogen angles: 1673 Unresolved non-hydrogen dihedrals: 1080 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 19, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 33, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 717 Chain: "B" Number of atoms: 16304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2185, 16304 Classifications: {'peptide': 2185} Incomplete info: {'truncation_to_alanine': 371} Link IDs: {'PTRANS': 86, 'TRANS': 2098} Chain breaks: 19 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1358 Unresolved non-hydrogen angles: 1727 Unresolved non-hydrogen dihedrals: 1114 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 19, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 21, 'GLU:plan': 34, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 738 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8931 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1079} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 8931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8931 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1079} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 842 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 842 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 21.73, per 1000 atoms: 0.38 Number of scatterers: 57117 At special positions: 0 Unit cell: (232.1, 232.1, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 334 16.00 O 10449 8.00 N 10168 7.00 C 36166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 18.43 Conformation dependent library (CDL) restraints added in 7.7 seconds 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14294 Finding SS restraints... Secondary structure from input PDB file: 437 helices and 22 sheets defined 70.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.528A pdb=" N ASP A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.510A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.923A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.252A pdb=" N MET A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.635A pdb=" N TYR A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 145' Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.696A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 164 through 178 removed outlier: 4.101A pdb=" N ALA A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.042A pdb=" N GLN A 185 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A 186 " --> pdb=" O PHE A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 186' Processing helix chain 'A' and resid 189 through 197 removed outlier: 4.014A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 204 through 223 removed outlier: 4.050A pdb=" N GLY A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 277 through 287 removed outlier: 4.165A pdb=" N ARG A 281 " --> pdb=" O MET A 277 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.771A pdb=" N MET A 366 " --> pdb=" O CYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 403 Proline residue: A 397 - end of helix removed outlier: 3.798A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.645A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 451 removed outlier: 3.818A pdb=" N PHE A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.309A pdb=" N VAL A 455 " --> pdb=" O TYR A 451 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 457' Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.872A pdb=" N ALA A 461 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 4.061A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.560A pdb=" N LYS A 502 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 503 " --> pdb=" O ASP A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 505 through 511 removed outlier: 3.662A pdb=" N LEU A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 581 through 590 removed outlier: 3.633A pdb=" N GLY A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 648 through 665 Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.700A pdb=" N ARG A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.584A pdb=" N PHE A 683 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 687 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.710A pdb=" N LEU A 693 " --> pdb=" O GLN A 689 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 720 removed outlier: 4.431A pdb=" N SER A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.619A pdb=" N VAL A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 764 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 771 through 784 removed outlier: 3.780A pdb=" N ILE A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 809 Processing helix chain 'A' and resid 816 through 829 removed outlier: 3.599A pdb=" N LEU A 820 " --> pdb=" O TRP A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 852 removed outlier: 3.860A pdb=" N ALA A 840 " --> pdb=" O LYS A 836 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.755A pdb=" N VAL A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 871 " --> pdb=" O VAL A 867 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 Processing helix chain 'A' and resid 895 through 902 Processing helix chain 'A' and resid 928 through 937 Processing helix chain 'A' and resid 942 through 945 Processing helix chain 'A' and resid 946 through 961 removed outlier: 3.509A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 983 removed outlier: 3.642A pdb=" N VAL A 971 " --> pdb=" O HIS A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.778A pdb=" N VAL A 987 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN A 988 " --> pdb=" O LYS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1004 Processing helix chain 'A' and resid 1007 through 1021 removed outlier: 3.759A pdb=" N PHE A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1041 removed outlier: 4.196A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A1034 " --> pdb=" O TYR A1030 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1036 " --> pdb=" O ASP A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1064 Processing helix chain 'A' and resid 1066 through 1073 Proline residue: A1072 - end of helix Processing helix chain 'A' and resid 1074 through 1084 removed outlier: 3.847A pdb=" N MET A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1102 removed outlier: 4.024A pdb=" N LEU A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.737A pdb=" N LEU A1107 " --> pdb=" O GLY A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1122 Proline residue: A1116 - end of helix removed outlier: 3.701A pdb=" N PHE A1122 " --> pdb=" O ILE A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1143 removed outlier: 4.139A pdb=" N THR A1143 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1163 removed outlier: 3.777A pdb=" N HIS A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1184 removed outlier: 3.518A pdb=" N PHE A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1190 removed outlier: 3.537A pdb=" N TYR A1188 " --> pdb=" O GLY A1185 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1201 removed outlier: 4.146A pdb=" N VAL A1198 " --> pdb=" O MET A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1228 through 1238 removed outlier: 3.571A pdb=" N TYR A1232 " --> pdb=" O ASP A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1269 removed outlier: 4.421A pdb=" N GLN A1266 " --> pdb=" O ILE A1263 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A1267 " --> pdb=" O ASN A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1294 removed outlier: 3.680A pdb=" N ASP A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1308 removed outlier: 3.993A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1317 removed outlier: 4.208A pdb=" N ALA A1314 " --> pdb=" O TYR A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1327 Processing helix chain 'A' and resid 1330 through 1348 Processing helix chain 'A' and resid 1350 through 1366 removed outlier: 3.525A pdb=" N HIS A1366 " --> pdb=" O GLU A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1390 removed outlier: 3.501A pdb=" N ALA A1388 " --> pdb=" O GLY A1384 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS A1389 " --> pdb=" O GLU A1385 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A1390 " --> pdb=" O ARG A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1407 removed outlier: 3.886A pdb=" N ALA A1396 " --> pdb=" O ALA A1392 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1423 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.664A pdb=" N ALA A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1454 Processing helix chain 'A' and resid 1455 through 1469 removed outlier: 3.880A pdb=" N THR A1469 " --> pdb=" O LYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1488 Processing helix chain 'A' and resid 1490 through 1501 Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 4.528A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1534 removed outlier: 3.646A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 Processing helix chain 'A' and resid 1558 through 1580 removed outlier: 4.388A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A1569 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY A1580 " --> pdb=" O THR A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1598 removed outlier: 4.666A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A1592 " --> pdb=" O GLY A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1598 through 1608 Processing helix chain 'A' and resid 1611 through 1624 removed outlier: 3.562A pdb=" N TRP A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1641 removed outlier: 4.109A pdb=" N LYS A1635 " --> pdb=" O GLU A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1664 removed outlier: 4.189A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 removed outlier: 3.692A pdb=" N ALA A1669 " --> pdb=" O ARG A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1708 removed outlier: 3.556A pdb=" N THR A1697 " --> pdb=" O HIS A1693 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A1708 " --> pdb=" O MET A1704 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1725 removed outlier: 3.961A pdb=" N GLN A1715 " --> pdb=" O ILE A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1731 removed outlier: 4.005A pdb=" N GLN A1729 " --> pdb=" O GLN A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1763 removed outlier: 3.901A pdb=" N LEU A1743 " --> pdb=" O HIS A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1784 removed outlier: 4.233A pdb=" N LYS A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1808 removed outlier: 3.578A pdb=" N TRP A1790 " --> pdb=" O TRP A1786 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A1808 " --> pdb=" O TYR A1804 " (cutoff:3.500A) Processing helix chain 'A' and resid 1874 through 1896 Proline residue: A1883 - end of helix removed outlier: 3.708A pdb=" N ARG A1896 " --> pdb=" O ILE A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 Processing helix chain 'A' and resid 1916 through 1930 removed outlier: 3.636A pdb=" N GLU A1921 " --> pdb=" O PRO A1917 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1937 removed outlier: 3.708A pdb=" N GLN A1937 " --> pdb=" O THR A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1944 Processing helix chain 'A' and resid 1950 through 1968 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 4.604A pdb=" N TYR A1974 " --> pdb=" O GLN A1970 " (cutoff:3.500A) Proline residue: A1975 - end of helix removed outlier: 3.594A pdb=" N LYS A1981 " --> pdb=" O THR A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1999 Processing helix chain 'A' and resid 2003 through 2021 removed outlier: 4.363A pdb=" N ARG A2018 " --> pdb=" O GLU A2014 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A2019 " --> pdb=" O GLU A2015 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A2021 " --> pdb=" O ILE A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2042 removed outlier: 3.853A pdb=" N ARG A2036 " --> pdb=" O GLU A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2059 removed outlier: 3.650A pdb=" N MET A2047 " --> pdb=" O ASN A2043 " (cutoff:3.500A) Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2091 removed outlier: 6.167A pdb=" N ARG A2076 " --> pdb=" O GLN A2072 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A2082 " --> pdb=" O LEU A2078 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A2091 " --> pdb=" O LYS A2087 " (cutoff:3.500A) Processing helix chain 'A' and resid 2096 through 2113 removed outlier: 3.774A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A2113 " --> pdb=" O ARG A2109 " (cutoff:3.500A) Processing helix chain 'A' and resid 2114 through 2118 Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2192 through 2211 removed outlier: 3.557A pdb=" N ASN A2211 " --> pdb=" O THR A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2217 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 removed outlier: 3.778A pdb=" N LEU A2278 " --> pdb=" O TYR A2275 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2292 Processing helix chain 'A' and resid 2297 through 2306 removed outlier: 3.598A pdb=" N LYS A2301 " --> pdb=" O ASP A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2335 Processing helix chain 'A' and resid 2380 through 2386 removed outlier: 3.630A pdb=" N ALA A2386 " --> pdb=" O MET A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 removed outlier: 3.739A pdb=" N ILE A2398 " --> pdb=" O GLY A2394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A2410 " --> pdb=" O VAL A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.749A pdb=" N VAL A2414 " --> pdb=" O HIS A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2510 removed outlier: 3.850A pdb=" N ARG A2503 " --> pdb=" O GLN A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2533 Processing helix chain 'A' and resid 2534 through 2539 Processing helix chain 'A' and resid 2540 through 2541 No H-bonds generated for 'chain 'A' and resid 2540 through 2541' Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'B' and resid 19 through 30 removed outlier: 4.382A pdb=" N LYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.898A pdb=" N LEU B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.632A pdb=" N LEU B 74 " --> pdb=" O HIS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.653A pdb=" N LEU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.770A pdb=" N GLY B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 140 through 150 removed outlier: 4.715A pdb=" N VAL B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.640A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 179 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.649A pdb=" N GLN B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.913A pdb=" N PHE B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 204 through 222 removed outlier: 3.523A pdb=" N GLY B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 261 through 276 Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 359 through 361 No H-bonds generated for 'chain 'B' and resid 359 through 361' Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 387 through 403 Proline residue: B 397 - end of helix removed outlier: 4.035A pdb=" N ARG B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 426 removed outlier: 4.299A pdb=" N LYS B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 450 through 459 removed outlier: 3.951A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.906A pdb=" N THR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 511 removed outlier: 4.553A pdb=" N LEU B 504 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 531 through 548 removed outlier: 3.505A pdb=" N ILE B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 600 through 606 removed outlier: 4.185A pdb=" N ARG B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 removed outlier: 4.318A pdb=" N PHE B 610 " --> pdb=" O CYS B 606 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 611' Processing helix chain 'B' and resid 615 through 630 removed outlier: 4.126A pdb=" N LEU B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 666 removed outlier: 3.588A pdb=" N VAL B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 679 removed outlier: 3.697A pdb=" N ARG B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.545A pdb=" N PHE B 683 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA B 685 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 701 removed outlier: 4.239A pdb=" N ASN B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 719 removed outlier: 3.529A pdb=" N ARG B 708 " --> pdb=" O VAL B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 744 removed outlier: 3.967A pdb=" N VAL B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 746 through 764 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 771 through 784 removed outlier: 3.639A pdb=" N ILE B 775 " --> pdb=" O TYR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 809 Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 816 through 829 Processing helix chain 'B' and resid 836 through 852 removed outlier: 3.532A pdb=" N ALA B 840 " --> pdb=" O LYS B 836 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL B 848 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 849 " --> pdb=" O GLY B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 4.410A pdb=" N ARG B 859 " --> pdb=" O VAL B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 875 removed outlier: 3.528A pdb=" N VAL B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 892 Processing helix chain 'B' and resid 895 through 902 Processing helix chain 'B' and resid 929 through 935 removed outlier: 4.247A pdb=" N GLU B 933 " --> pdb=" O TYR B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 3.531A pdb=" N PHE B 946 " --> pdb=" O PRO B 942 " (cutoff:3.500A) Proline residue: B 948 - end of helix removed outlier: 3.618A pdb=" N ILE B 958 " --> pdb=" O ALA B 954 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B 961 " --> pdb=" O ARG B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 983 removed outlier: 3.569A pdb=" N VAL B 971 " --> pdb=" O HIS B 967 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 983 " --> pdb=" O PHE B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 990 removed outlier: 3.949A pdb=" N VAL B 987 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN B 988 " --> pdb=" O LYS B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.512A pdb=" N PHE B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1023 removed outlier: 3.655A pdb=" N PHE B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B1023 " --> pdb=" O LEU B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1041 removed outlier: 4.173A pdb=" N ASP B1032 " --> pdb=" O ARG B1028 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B1033 " --> pdb=" O PRO B1029 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE B1034 " --> pdb=" O TYR B1030 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B1036 " --> pdb=" O ASP B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1064 removed outlier: 3.888A pdb=" N LEU B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1073 Proline residue: B1072 - end of helix Processing helix chain 'B' and resid 1074 through 1084 removed outlier: 3.517A pdb=" N MET B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B1082 " --> pdb=" O MET B1078 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET B1083 " --> pdb=" O LEU B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'B' and resid 1090 through 1101 Processing helix chain 'B' and resid 1102 through 1107 removed outlier: 6.029A pdb=" N ALA B1105 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B1107 " --> pdb=" O GLY B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1123 Proline residue: B1116 - end of helix Processing helix chain 'B' and resid 1128 through 1143 removed outlier: 3.655A pdb=" N THR B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1164 removed outlier: 3.627A pdb=" N HIS B1157 " --> pdb=" O SER B1153 " (cutoff:3.500A) Proline residue: B1158 - end of helix removed outlier: 4.226A pdb=" N ASP B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1168 removed outlier: 6.557A pdb=" N GLU B1168 " --> pdb=" O GLN B1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1165 through 1168' Processing helix chain 'B' and resid 1169 through 1184 removed outlier: 3.795A pdb=" N GLN B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1190 removed outlier: 4.433A pdb=" N ILE B1190 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1203 removed outlier: 3.875A pdb=" N VAL B1195 " --> pdb=" O PHE B1191 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS B1202 " --> pdb=" O VAL B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1218 Processing helix chain 'B' and resid 1228 through 1238 Processing helix chain 'B' and resid 1264 through 1270 removed outlier: 3.778A pdb=" N ALA B1268 " --> pdb=" O ASN B1264 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1294 removed outlier: 3.967A pdb=" N ASP B1294 " --> pdb=" O GLU B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1310 removed outlier: 4.006A pdb=" N ALA B1305 " --> pdb=" O ARG B1301 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B1306 " --> pdb=" O SER B1302 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B1309 " --> pdb=" O ALA B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1317 removed outlier: 4.341A pdb=" N ALA B1314 " --> pdb=" O TYR B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1328 removed outlier: 3.580A pdb=" N ALA B1321 " --> pdb=" O LEU B1317 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B1328 " --> pdb=" O SER B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1348 removed outlier: 3.666A pdb=" N GLN B1348 " --> pdb=" O ALA B1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1366 Processing helix chain 'B' and resid 1376 through 1378 No H-bonds generated for 'chain 'B' and resid 1376 through 1378' Processing helix chain 'B' and resid 1379 through 1389 removed outlier: 4.050A pdb=" N LYS B1389 " --> pdb=" O GLU B1385 " (cutoff:3.500A) Processing helix chain 'B' and resid 1392 through 1407 removed outlier: 4.558A pdb=" N LYS B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B1407 " --> pdb=" O GLU B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1409 through 1422 Processing helix chain 'B' and resid 1425 through 1440 removed outlier: 3.756A pdb=" N ALA B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1454 removed outlier: 3.749A pdb=" N TYR B1450 " --> pdb=" O GLN B1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1468 Processing helix chain 'B' and resid 1476 through 1488 removed outlier: 3.813A pdb=" N ARG B1480 " --> pdb=" O LEU B1476 " (cutoff:3.500A) Processing helix chain 'B' and resid 1490 through 1502 removed outlier: 3.719A pdb=" N GLU B1499 " --> pdb=" O GLN B1495 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR B1502 " --> pdb=" O CYS B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1505 through 1524 removed outlier: 4.239A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1525 through 1534 removed outlier: 3.558A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS B1534 " --> pdb=" O GLU B1530 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1554 Processing helix chain 'B' and resid 1558 through 1580 removed outlier: 4.163A pdb=" N GLN B1562 " --> pdb=" O SER B1558 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B1569 " --> pdb=" O ASP B1565 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B1580 " --> pdb=" O THR B1576 " (cutoff:3.500A) Processing helix chain 'B' and resid 1582 through 1608 removed outlier: 4.166A pdb=" N GLY B1588 " --> pdb=" O SER B1584 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA B1589 " --> pdb=" O ARG B1585 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER B1592 " --> pdb=" O GLY B1588 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B1598 " --> pdb=" O HIS B1594 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B1599 " --> pdb=" O MET B1595 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU B1600 " --> pdb=" O LEU B1596 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU B1601 " --> pdb=" O SER B1597 " (cutoff:3.500A) Processing helix chain 'B' and resid 1611 through 1624 removed outlier: 3.511A pdb=" N TRP B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) Processing helix chain 'B' and resid 1629 through 1641 removed outlier: 3.519A pdb=" N TRP B1633 " --> pdb=" O ILE B1629 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B1635 " --> pdb=" O GLU B1631 " (cutoff:3.500A) Processing helix chain 'B' and resid 1645 through 1648 Processing helix chain 'B' and resid 1649 through 1664 removed outlier: 4.240A pdb=" N TRP B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1678 removed outlier: 3.611A pdb=" N ALA B1669 " --> pdb=" O ARG B1665 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1708 removed outlier: 3.704A pdb=" N THR B1697 " --> pdb=" O HIS B1693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B1708 " --> pdb=" O MET B1704 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1731 removed outlier: 3.662A pdb=" N GLN B1715 " --> pdb=" O ILE B1711 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B1726 " --> pdb=" O GLN B1722 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B1727 " --> pdb=" O THR B1723 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B1728 " --> pdb=" O MET B1724 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN B1729 " --> pdb=" O GLN B1725 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1763 Processing helix chain 'B' and resid 1767 through 1784 removed outlier: 4.199A pdb=" N LYS B1771 " --> pdb=" O SER B1767 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1808 removed outlier: 3.708A pdb=" N TRP B1790 " --> pdb=" O TRP B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1874 through 1896 Proline residue: B1883 - end of helix removed outlier: 3.670A pdb=" N ARG B1896 " --> pdb=" O ILE B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1899 through 1914 removed outlier: 3.634A pdb=" N THR B1903 " --> pdb=" O ASN B1899 " (cutoff:3.500A) Processing helix chain 'B' and resid 1916 through 1930 removed outlier: 3.812A pdb=" N LYS B1928 " --> pdb=" O VAL B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1932 through 1937 removed outlier: 3.637A pdb=" N GLN B1937 " --> pdb=" O THR B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1945 removed outlier: 3.692A pdb=" N ARG B1945 " --> pdb=" O GLN B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1968 Processing helix chain 'B' and resid 1969 through 1981 removed outlier: 4.705A pdb=" N TYR B1974 " --> pdb=" O GLN B1970 " (cutoff:3.500A) Proline residue: B1975 - end of helix removed outlier: 3.554A pdb=" N LYS B1981 " --> pdb=" O THR B1977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 1999 Processing helix chain 'B' and resid 2003 through 2021 removed outlier: 4.284A pdb=" N ARG B2018 " --> pdb=" O GLU B2014 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B2019 " --> pdb=" O GLU B2015 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B2021 " --> pdb=" O ILE B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2042 removed outlier: 3.791A pdb=" N ARG B2036 " --> pdb=" O GLU B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2043 through 2059 removed outlier: 3.590A pdb=" N MET B2047 " --> pdb=" O ASN B2043 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU B2049 " --> pdb=" O LYS B2045 " (cutoff:3.500A) Proline residue: B2053 - end of helix Processing helix chain 'B' and resid 2064 through 2091 removed outlier: 6.194A pdb=" N ARG B2076 " --> pdb=" O GLN B2072 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B2077 " --> pdb=" O ALA B2073 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B2082 " --> pdb=" O LEU B2078 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2113 removed outlier: 4.152A pdb=" N LEU B2097 " --> pdb=" O ASN B2093 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B2099 " --> pdb=" O LYS B2095 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B2113 " --> pdb=" O ARG B2109 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2118 Processing helix chain 'B' and resid 2123 through 2127 Processing helix chain 'B' and resid 2129 through 2133 Processing helix chain 'B' and resid 2192 through 2211 removed outlier: 3.589A pdb=" N ASN B2211 " --> pdb=" O THR B2207 " (cutoff:3.500A) Processing helix chain 'B' and resid 2212 through 2217 removed outlier: 3.518A pdb=" N ARG B2217 " --> pdb=" O PRO B2213 " (cutoff:3.500A) Processing helix chain 'B' and resid 2246 through 2257 Processing helix chain 'B' and resid 2262 through 2272 Processing helix chain 'B' and resid 2274 through 2278 Processing helix chain 'B' and resid 2279 through 2292 Processing helix chain 'B' and resid 2297 through 2306 removed outlier: 3.526A pdb=" N LYS B2301 " --> pdb=" O ASP B2297 " (cutoff:3.500A) Processing helix chain 'B' and resid 2309 through 2335 Processing helix chain 'B' and resid 2380 through 2388 removed outlier: 3.713A pdb=" N MET B2387 " --> pdb=" O LEU B2383 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU B2388 " --> pdb=" O THR B2384 " (cutoff:3.500A) Processing helix chain 'B' and resid 2394 through 2410 removed outlier: 3.792A pdb=" N ILE B2398 " --> pdb=" O GLY B2394 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS B2410 " --> pdb=" O VAL B2406 " (cutoff:3.500A) Processing helix chain 'B' and resid 2410 through 2423 removed outlier: 3.813A pdb=" N VAL B2414 " --> pdb=" O HIS B2410 " (cutoff:3.500A) Processing helix chain 'B' and resid 2494 through 2509 removed outlier: 3.744A pdb=" N LEU B2508 " --> pdb=" O VAL B2504 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2533 Processing helix chain 'B' and resid 2534 through 2539 Processing helix chain 'B' and resid 2540 through 2541 No H-bonds generated for 'chain 'B' and resid 2540 through 2541' Processing helix chain 'B' and resid 2542 through 2546 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 52 through 70 Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 80 through 90 removed outlier: 4.178A pdb=" N ILE E 84 " --> pdb=" O HIS E 80 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 96 through 111 removed outlier: 3.708A pdb=" N TYR E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.577A pdb=" N LEU E 123 " --> pdb=" O LYS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 removed outlier: 4.183A pdb=" N LEU E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 158 Processing helix chain 'E' and resid 162 through 175 removed outlier: 3.865A pdb=" N THR E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.852A pdb=" N LEU E 196 " --> pdb=" O CYS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.871A pdb=" N VAL E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 217 removed outlier: 3.935A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 235 removed outlier: 3.630A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 273 through 292 Processing helix chain 'E' and resid 294 through 302 Processing helix chain 'E' and resid 307 through 317 removed outlier: 3.520A pdb=" N SER E 311 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 336 removed outlier: 4.069A pdb=" N LEU E 328 " --> pdb=" O ARG E 324 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 353 removed outlier: 3.727A pdb=" N ALA E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 362 Processing helix chain 'E' and resid 363 through 368 removed outlier: 3.516A pdb=" N GLY E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 363 through 368' Processing helix chain 'E' and resid 369 through 377 removed outlier: 3.525A pdb=" N LEU E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 402 removed outlier: 3.753A pdb=" N ASN E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 removed outlier: 3.752A pdb=" N GLY E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 438 removed outlier: 4.193A pdb=" N ARG E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR E 436 " --> pdb=" O HIS E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 445 through 448 Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.530A pdb=" N ALA E 457 " --> pdb=" O MET E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 486 removed outlier: 3.856A pdb=" N ARG E 466 " --> pdb=" O PRO E 462 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY E 486 " --> pdb=" O MET E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 509 removed outlier: 3.815A pdb=" N ASP E 495 " --> pdb=" O SER E 491 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP E 509 " --> pdb=" O HIS E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 535 Processing helix chain 'E' and resid 547 through 557 Processing helix chain 'E' and resid 567 through 582 Processing helix chain 'E' and resid 583 through 586 Processing helix chain 'E' and resid 598 through 615 Processing helix chain 'E' and resid 619 through 639 removed outlier: 3.981A pdb=" N LEU E 623 " --> pdb=" O GLY E 619 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 626 " --> pdb=" O TYR E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 652 removed outlier: 4.018A pdb=" N LEU E 651 " --> pdb=" O GLN E 647 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 652 " --> pdb=" O ASN E 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 647 through 652' Processing helix chain 'E' and resid 654 through 657 removed outlier: 3.625A pdb=" N GLN E 657 " --> pdb=" O THR E 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 654 through 657' Processing helix chain 'E' and resid 658 through 667 removed outlier: 4.181A pdb=" N PHE E 662 " --> pdb=" O HIS E 658 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE E 663 " --> pdb=" O TYR E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 679 removed outlier: 3.653A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS E 679 " --> pdb=" O MET E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 690 removed outlier: 3.672A pdb=" N SER E 690 " --> pdb=" O LEU E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 695 through 703 removed outlier: 3.532A pdb=" N LYS E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 703 " --> pdb=" O LYS E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 723 removed outlier: 4.080A pdb=" N VAL E 715 " --> pdb=" O GLY E 711 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 716 " --> pdb=" O LEU E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 735 Processing helix chain 'E' and resid 736 through 742 Processing helix chain 'E' and resid 746 through 759 removed outlier: 4.343A pdb=" N TRP E 750 " --> pdb=" O PHE E 746 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU E 753 " --> pdb=" O ASN E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 778 Processing helix chain 'E' and resid 780 through 789 Processing helix chain 'E' and resid 798 through 807 Processing helix chain 'E' and resid 808 through 810 No H-bonds generated for 'chain 'E' and resid 808 through 810' Processing helix chain 'E' and resid 811 through 820 removed outlier: 6.605A pdb=" N TYR E 817 " --> pdb=" O LYS E 813 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 820 " --> pdb=" O SER E 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 834 removed outlier: 3.710A pdb=" N GLU E 829 " --> pdb=" O ALA E 825 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS E 830 " --> pdb=" O LYS E 826 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 852 removed outlier: 3.656A pdb=" N LYS E 838 " --> pdb=" O GLU E 834 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 840 " --> pdb=" O ASN E 836 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 887 removed outlier: 3.697A pdb=" N VAL E 887 " --> pdb=" O TYR E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 890 No H-bonds generated for 'chain 'E' and resid 888 through 890' Processing helix chain 'E' and resid 891 through 898 Processing helix chain 'E' and resid 900 through 911 removed outlier: 4.404A pdb=" N GLU E 904 " --> pdb=" O ASN E 900 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 905 " --> pdb=" O ILE E 901 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 934 Processing helix chain 'E' and resid 936 through 945 removed outlier: 3.786A pdb=" N ASN E 941 " --> pdb=" O ASN E 937 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU E 945 " --> pdb=" O ASN E 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 948 through 959 Processing helix chain 'E' and resid 961 through 975 Processing helix chain 'E' and resid 978 through 987 removed outlier: 3.649A pdb=" N CYS E 987 " --> pdb=" O ASP E 983 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1438 removed outlier: 3.554A pdb=" N ILE E1436 " --> pdb=" O ILE E1433 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN E1438 " --> pdb=" O ASP E1435 " (cutoff:3.500A) Processing helix chain 'E' and resid 1444 through 1448 removed outlier: 3.673A pdb=" N THR E1447 " --> pdb=" O TYR E1444 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS E1448 " --> pdb=" O PHE E1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1444 through 1448' Processing helix chain 'E' and resid 1480 through 1485 removed outlier: 3.675A pdb=" N GLN E1485 " --> pdb=" O LEU E1482 " (cutoff:3.500A) Processing helix chain 'E' and resid 1488 through 1493 Processing helix chain 'E' and resid 1524 through 1529 removed outlier: 4.312A pdb=" N ILE E1528 " --> pdb=" O VAL E1524 " (cutoff:3.500A) Processing helix chain 'E' and resid 1609 through 1626 removed outlier: 3.996A pdb=" N SER E1625 " --> pdb=" O ILE E1621 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER E1626 " --> pdb=" O ASN E1622 " (cutoff:3.500A) Processing helix chain 'E' and resid 1628 through 1643 removed outlier: 3.858A pdb=" N HIS E1632 " --> pdb=" O SER E1628 " (cutoff:3.500A) Processing helix chain 'E' and resid 1644 through 1648 removed outlier: 4.023A pdb=" N PHE E1647 " --> pdb=" O PRO E1644 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP E1648 " --> pdb=" O GLN E1645 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1644 through 1648' Processing helix chain 'E' and resid 1649 through 1661 removed outlier: 3.709A pdb=" N TYR E1653 " --> pdb=" O ASP E1649 " (cutoff:3.500A) Processing helix chain 'E' and resid 1666 through 1676 Processing helix chain 'E' and resid 1682 through 1694 removed outlier: 3.698A pdb=" N HIS E1686 " --> pdb=" O PHE E1682 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA E1694 " --> pdb=" O GLU E1690 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 52 through 70 Processing helix chain 'F' and resid 73 through 78 Processing helix chain 'F' and resid 80 through 90 removed outlier: 4.178A pdb=" N ILE F 84 " --> pdb=" O HIS F 80 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 96 through 111 removed outlier: 3.708A pdb=" N TYR F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.577A pdb=" N LEU F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 removed outlier: 4.183A pdb=" N LEU F 128 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 162 through 175 removed outlier: 3.865A pdb=" N THR F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.852A pdb=" N LEU F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.871A pdb=" N VAL F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 217 removed outlier: 3.935A pdb=" N ILE F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 235 removed outlier: 3.631A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 273 through 292 Processing helix chain 'F' and resid 294 through 302 Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.521A pdb=" N SER F 311 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS F 317 " --> pdb=" O ILE F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 336 removed outlier: 4.068A pdb=" N LEU F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 353 removed outlier: 3.726A pdb=" N ALA F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 362 Processing helix chain 'F' and resid 363 through 368 removed outlier: 3.515A pdb=" N GLY F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE F 368 " --> pdb=" O LEU F 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 363 through 368' Processing helix chain 'F' and resid 369 through 377 removed outlier: 3.525A pdb=" N LEU F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 402 removed outlier: 3.754A pdb=" N ASN F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 414 removed outlier: 3.752A pdb=" N GLY F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 438 removed outlier: 4.193A pdb=" N ARG F 422 " --> pdb=" O HIS F 418 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR F 436 " --> pdb=" O HIS F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 445 through 448 Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.530A pdb=" N ALA F 457 " --> pdb=" O MET F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 486 removed outlier: 3.856A pdb=" N ARG F 466 " --> pdb=" O PRO F 462 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 486 " --> pdb=" O MET F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 509 removed outlier: 3.816A pdb=" N ASP F 495 " --> pdb=" O SER F 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP F 509 " --> pdb=" O HIS F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 Processing helix chain 'F' and resid 547 through 557 Processing helix chain 'F' and resid 567 through 582 Processing helix chain 'F' and resid 583 through 586 Processing helix chain 'F' and resid 598 through 615 Processing helix chain 'F' and resid 619 through 639 removed outlier: 3.980A pdb=" N LEU F 623 " --> pdb=" O GLY F 619 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F 626 " --> pdb=" O TYR F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 652 removed outlier: 4.020A pdb=" N LEU F 651 " --> pdb=" O GLN F 647 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU F 652 " --> pdb=" O ASN F 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 647 through 652' Processing helix chain 'F' and resid 654 through 657 removed outlier: 3.624A pdb=" N GLN F 657 " --> pdb=" O THR F 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 654 through 657' Processing helix chain 'F' and resid 658 through 667 removed outlier: 4.180A pdb=" N PHE F 662 " --> pdb=" O HIS F 658 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE F 663 " --> pdb=" O TYR F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 679 removed outlier: 3.654A pdb=" N LYS F 674 " --> pdb=" O PRO F 670 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS F 679 " --> pdb=" O MET F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 681 through 690 removed outlier: 3.672A pdb=" N SER F 690 " --> pdb=" O LEU F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 703 removed outlier: 3.531A pdb=" N LYS F 699 " --> pdb=" O ASP F 695 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER F 703 " --> pdb=" O LYS F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 723 removed outlier: 4.080A pdb=" N VAL F 715 " --> pdb=" O GLY F 711 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 735 Processing helix chain 'F' and resid 736 through 742 Processing helix chain 'F' and resid 746 through 759 removed outlier: 4.343A pdb=" N TRP F 750 " --> pdb=" O PHE F 746 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU F 753 " --> pdb=" O ASN F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 778 Processing helix chain 'F' and resid 780 through 789 Processing helix chain 'F' and resid 798 through 807 Processing helix chain 'F' and resid 808 through 810 No H-bonds generated for 'chain 'F' and resid 808 through 810' Processing helix chain 'F' and resid 811 through 820 removed outlier: 6.604A pdb=" N TYR F 817 " --> pdb=" O LYS F 813 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU F 820 " --> pdb=" O SER F 816 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 834 removed outlier: 3.710A pdb=" N GLU F 829 " --> pdb=" O ALA F 825 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS F 830 " --> pdb=" O LYS F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 834 through 852 removed outlier: 3.656A pdb=" N LYS F 838 " --> pdb=" O GLU F 834 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 840 " --> pdb=" O ASN F 836 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 887 removed outlier: 3.697A pdb=" N VAL F 887 " --> pdb=" O TYR F 883 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 890 No H-bonds generated for 'chain 'F' and resid 888 through 890' Processing helix chain 'F' and resid 891 through 898 Processing helix chain 'F' and resid 900 through 911 removed outlier: 4.403A pdb=" N GLU F 904 " --> pdb=" O ASN F 900 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU F 905 " --> pdb=" O ILE F 901 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 934 Processing helix chain 'F' and resid 936 through 945 removed outlier: 3.786A pdb=" N ASN F 941 " --> pdb=" O ASN F 937 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU F 945 " --> pdb=" O ASN F 941 " (cutoff:3.500A) Processing helix chain 'F' and resid 948 through 959 Processing helix chain 'F' and resid 961 through 975 Processing helix chain 'F' and resid 978 through 987 removed outlier: 3.650A pdb=" N CYS F 987 " --> pdb=" O ASP F 983 " (cutoff:3.500A) Processing helix chain 'F' and resid 1432 through 1438 removed outlier: 3.554A pdb=" N ILE F1436 " --> pdb=" O ILE F1433 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN F1438 " --> pdb=" O ASP F1435 " (cutoff:3.500A) Processing helix chain 'F' and resid 1444 through 1448 removed outlier: 3.672A pdb=" N THR F1447 " --> pdb=" O TYR F1444 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS F1448 " --> pdb=" O PHE F1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1444 through 1448' Processing helix chain 'F' and resid 1480 through 1485 removed outlier: 3.674A pdb=" N GLN F1485 " --> pdb=" O LEU F1482 " (cutoff:3.500A) Processing helix chain 'F' and resid 1488 through 1493 Processing helix chain 'F' and resid 1524 through 1529 removed outlier: 4.313A pdb=" N ILE F1528 " --> pdb=" O VAL F1524 " (cutoff:3.500A) Processing helix chain 'F' and resid 1609 through 1626 removed outlier: 3.996A pdb=" N SER F1625 " --> pdb=" O ILE F1621 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER F1626 " --> pdb=" O ASN F1622 " (cutoff:3.500A) Processing helix chain 'F' and resid 1628 through 1643 removed outlier: 3.857A pdb=" N HIS F1632 " --> pdb=" O SER F1628 " (cutoff:3.500A) Processing helix chain 'F' and resid 1644 through 1648 removed outlier: 4.022A pdb=" N PHE F1647 " --> pdb=" O PRO F1644 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP F1648 " --> pdb=" O GLN F1645 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1644 through 1648' Processing helix chain 'F' and resid 1649 through 1661 removed outlier: 3.707A pdb=" N TYR F1653 " --> pdb=" O ASP F1649 " (cutoff:3.500A) Processing helix chain 'F' and resid 1666 through 1676 Processing helix chain 'F' and resid 1682 through 1694 removed outlier: 3.700A pdb=" N HIS F1686 " --> pdb=" O PHE F1682 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA F1694 " --> pdb=" O GLU F1690 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 removed outlier: 3.748A pdb=" N ILE G 10 " --> pdb=" O ASN G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 66 through 72 removed outlier: 4.027A pdb=" N ASP G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 101 removed outlier: 3.595A pdb=" N ASN G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 4.170A pdb=" N PHE G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'H' and resid 6 through 21 removed outlier: 3.748A pdb=" N ILE H 10 " --> pdb=" O ASN H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 31 Processing helix chain 'H' and resid 66 through 72 removed outlier: 4.027A pdb=" N ASP H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 101 removed outlier: 3.596A pdb=" N ASN H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 124 removed outlier: 4.170A pdb=" N PHE H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 3.976A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.589A pdb=" N SER A2234 " --> pdb=" O LEU A2230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'B' and resid 2120 through 2122 removed outlier: 4.549A pdb=" N GLN B2161 " --> pdb=" O LYS B2171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2153 through 2156 removed outlier: 6.719A pdb=" N MET B2175 " --> pdb=" O GLN B2154 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE B2156 " --> pdb=" O THR B2173 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR B2173 " --> pdb=" O ILE B2156 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER B2234 " --> pdb=" O LEU B2230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 39 removed outlier: 3.944A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 321 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS C 317 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.646A pdb=" N HIS C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE G 106 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 93 removed outlier: 3.617A pdb=" N SER C 90 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB2, first strand: chain 'C' and resid 173 through 177 removed outlier: 7.020A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 223 through 227 removed outlier: 3.515A pdb=" N GLN C 225 " --> pdb=" O CYS C 238 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 273 through 277 Processing sheet with id=AB5, first strand: chain 'D' and resid 34 through 39 removed outlier: 3.944A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN D 321 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS D 317 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.645A pdb=" N HIS D 64 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 93 removed outlier: 3.616A pdb=" N SER D 90 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB9, first strand: chain 'D' and resid 173 through 177 removed outlier: 7.019A pdb=" N VAL D 188 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA D 176 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA D 186 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN D 193 " --> pdb=" O ASN D 189 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN D 198 " --> pdb=" O PRO D 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 223 through 227 removed outlier: 3.514A pdb=" N GLN D 225 " --> pdb=" O CYS D 238 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 273 through 277 Processing sheet with id=AC3, first strand: chain 'E' and resid 990 through 991 Processing sheet with id=AC4, first strand: chain 'F' and resid 990 through 991 3291 hydrogen bonds defined for protein. 9642 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: 25.36 Time building geometry restraints manager: 20.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.19: 44 1.19 - 1.35: 19221 1.35 - 1.50: 15343 1.50 - 1.66: 23032 1.66 - 1.82: 524 Bond restraints: 58164 Sorted by residual: bond pdb=" CA ASN H 85 " pdb=" C ASN H 85 " ideal model delta sigma weight residual 1.523 1.279 0.244 1.34e-02 5.57e+03 3.33e+02 bond pdb=" CA ASN G 85 " pdb=" C ASN G 85 " ideal model delta sigma weight residual 1.523 1.280 0.243 1.34e-02 5.57e+03 3.30e+02 bond pdb=" N ALA H 87 " pdb=" CA ALA H 87 " ideal model delta sigma weight residual 1.459 1.249 0.210 1.19e-02 7.06e+03 3.12e+02 bond pdb=" N ALA G 87 " pdb=" CA ALA G 87 " ideal model delta sigma weight residual 1.459 1.250 0.210 1.19e-02 7.06e+03 3.11e+02 bond pdb=" C THR G 86 " pdb=" O THR G 86 " ideal model delta sigma weight residual 1.235 1.441 -0.206 1.26e-02 6.30e+03 2.67e+02 ... (remaining 58159 not shown) Histogram of bond angle deviations from ideal: 78.05 - 93.67: 8 93.67 - 109.28: 4882 109.28 - 124.89: 72930 124.89 - 140.51: 1121 140.51 - 156.12: 2 Bond angle restraints: 78943 Sorted by residual: angle pdb=" C GLN H 88 " pdb=" N ARG H 89 " pdb=" CA ARG H 89 " ideal model delta sigma weight residual 120.44 92.61 27.83 1.30e+00 5.92e-01 4.58e+02 angle pdb=" C GLN G 88 " pdb=" N ARG G 89 " pdb=" CA ARG G 89 " ideal model delta sigma weight residual 120.44 92.63 27.81 1.30e+00 5.92e-01 4.58e+02 angle pdb=" N ASP H 77 " pdb=" CA ASP H 77 " pdb=" C ASP H 77 " ideal model delta sigma weight residual 110.80 156.12 -45.32 2.13e+00 2.20e-01 4.53e+02 angle pdb=" N ASP G 77 " pdb=" CA ASP G 77 " pdb=" C ASP G 77 " ideal model delta sigma weight residual 110.80 156.08 -45.28 2.13e+00 2.20e-01 4.52e+02 angle pdb=" C ASP G 77 " pdb=" CA ASP G 77 " pdb=" CB ASP G 77 " ideal model delta sigma weight residual 110.42 78.05 32.37 1.99e+00 2.53e-01 2.65e+02 ... (remaining 78938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 31853 17.98 - 35.95: 2689 35.95 - 53.93: 414 53.93 - 71.91: 131 71.91 - 89.89: 60 Dihedral angle restraints: 35147 sinusoidal: 13243 harmonic: 21904 Sorted by residual: dihedral pdb=" C ASP G 77 " pdb=" N ASP G 77 " pdb=" CA ASP G 77 " pdb=" CB ASP G 77 " ideal model delta harmonic sigma weight residual -122.60 -73.18 -49.42 0 2.50e+00 1.60e-01 3.91e+02 dihedral pdb=" C ASP H 77 " pdb=" N ASP H 77 " pdb=" CA ASP H 77 " pdb=" CB ASP H 77 " ideal model delta harmonic sigma weight residual -122.60 -73.18 -49.42 0 2.50e+00 1.60e-01 3.91e+02 dihedral pdb=" C ASN G 85 " pdb=" N ASN G 85 " pdb=" CA ASN G 85 " pdb=" CB ASN G 85 " ideal model delta harmonic sigma weight residual -122.60 -169.54 46.94 0 2.50e+00 1.60e-01 3.52e+02 ... (remaining 35144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.441: 9126 0.441 - 0.881: 20 0.881 - 1.322: 8 1.322 - 1.762: 0 1.762 - 2.203: 4 Chirality restraints: 9158 Sorted by residual: chirality pdb=" CA ASN G 85 " pdb=" N ASN G 85 " pdb=" C ASN G 85 " pdb=" CB ASN G 85 " both_signs ideal model delta sigma weight residual False 2.51 0.31 2.20 2.00e-01 2.50e+01 1.21e+02 chirality pdb=" CA ASN H 85 " pdb=" N ASN H 85 " pdb=" C ASN H 85 " pdb=" CB ASN H 85 " both_signs ideal model delta sigma weight residual False 2.51 0.31 2.20 2.00e-01 2.50e+01 1.21e+02 chirality pdb=" CA ILE G 80 " pdb=" N ILE G 80 " pdb=" C ILE G 80 " pdb=" CB ILE G 80 " both_signs ideal model delta sigma weight residual False 2.43 0.64 1.79 2.00e-01 2.50e+01 8.01e+01 ... (remaining 9155 not shown) Planarity restraints: 10144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 77 " -0.065 2.00e-02 2.50e+03 1.24e-01 1.53e+02 pdb=" CG ASP H 77 " 0.213 2.00e-02 2.50e+03 pdb=" OD1 ASP H 77 " -0.062 2.00e-02 2.50e+03 pdb=" OD2 ASP H 77 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 77 " -0.065 2.00e-02 2.50e+03 1.23e-01 1.52e+02 pdb=" CG ASP G 77 " 0.213 2.00e-02 2.50e+03 pdb=" OD1 ASP G 77 " -0.061 2.00e-02 2.50e+03 pdb=" OD2 ASP G 77 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 36 " -0.049 2.00e-02 2.50e+03 1.14e-01 1.30e+02 pdb=" C VAL G 36 " 0.196 2.00e-02 2.50e+03 pdb=" O VAL G 36 " -0.082 2.00e-02 2.50e+03 pdb=" N ASP G 37 " -0.065 2.00e-02 2.50e+03 ... (remaining 10141 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 16 1.92 - 2.67: 1304 2.67 - 3.41: 88875 3.41 - 4.16: 128498 4.16 - 4.90: 227198 Nonbonded interactions: 445891 Sorted by model distance: nonbonded pdb=" O SER G 84 " pdb=" N THR G 86 " model vdw 1.176 2.520 nonbonded pdb=" O SER H 84 " pdb=" N THR H 86 " model vdw 1.176 2.520 nonbonded pdb=" O THR H 86 " pdb=" CB ARG H 89 " model vdw 1.524 3.440 nonbonded pdb=" O THR G 86 " pdb=" CB ARG G 89 " model vdw 1.525 3.440 nonbonded pdb=" O ALA G 87 " pdb=" N LEU G 90 " model vdw 1.712 2.520 ... (remaining 445886 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 17 through 580 or (resid 581 through 589 and (name N or na \ me CA or name C or name O or name CB )) or resid 590 or (resid 591 through 595 a \ nd (name N or name CA or name C or name O or name CB )) or resid 599 through 254 \ 9)) selection = (chain 'B' and (resid 17 through 578 or resid 580 through 2549)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 9.320 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 120.860 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.008 0.261 58164 Z= 0.526 Angle : 1.124 45.323 78943 Z= 0.651 Chirality : 0.079 2.203 9158 Planarity : 0.006 0.124 10144 Dihedral : 14.313 89.886 20853 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.60 % Favored : 93.07 % Rotamer: Outliers : 1.53 % Allowed : 0.69 % Favored : 97.78 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.06 (0.10), residues: 7360 helix: 0.06 (0.08), residues: 4517 sheet: -0.90 (0.26), residues: 355 loop : -2.01 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A1269 HIS 0.032 0.001 HIS A1112 PHE 0.057 0.002 PHE B1720 TYR 0.060 0.003 TYR G 66 ARG 0.036 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2024 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1936 time to evaluate : 4.743 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: A 650 GLN cc_start: 0.8664 (pt0) cc_final: 0.8015 (pt0) REVERT: A 818 ASP cc_start: 0.8894 (m-30) cc_final: 0.8672 (m-30) REVERT: A 964 LEU cc_start: 0.7341 (tp) cc_final: 0.7118 (tp) REVERT: A 1166 SER cc_start: 0.7876 (m) cc_final: 0.7032 (p) REVERT: A 1222 LEU cc_start: 0.6900 (mt) cc_final: 0.6151 (mt) REVERT: A 1269 TRP cc_start: 0.4541 (m-90) cc_final: 0.3564 (m-90) REVERT: A 1313 MET cc_start: 0.7678 (ppp) cc_final: 0.7154 (ppp) REVERT: A 1421 ASN cc_start: 0.8751 (t0) cc_final: 0.8516 (t0) REVERT: A 1466 LYS cc_start: 0.8496 (tptm) cc_final: 0.8093 (tppt) REVERT: A 1515 MET cc_start: 0.5807 (tmm) cc_final: 0.5315 (tmm) REVERT: A 1649 ASP cc_start: 0.7427 (t0) cc_final: 0.6379 (p0) REVERT: A 1738 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6318 (tm-30) REVERT: A 1793 TRP cc_start: 0.7874 (t60) cc_final: 0.7646 (t60) REVERT: A 1945 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7454 (tpp-160) REVERT: A 1959 GLN cc_start: 0.8437 (mp-120) cc_final: 0.8138 (mp10) REVERT: A 1993 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8663 (tmtt) REVERT: A 2338 ASP cc_start: 0.6678 (t0) cc_final: 0.6383 (t0) REVERT: A 2412 ASP cc_start: 0.8389 (m-30) cc_final: 0.8131 (m-30) REVERT: B 621 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7826 (tp30) REVERT: B 1222 LEU cc_start: 0.7197 (mt) cc_final: 0.6661 (mt) REVERT: B 1224 ASP cc_start: 0.8047 (m-30) cc_final: 0.7531 (t0) REVERT: B 1362 GLU cc_start: 0.8762 (tt0) cc_final: 0.8455 (tp30) REVERT: B 1369 LYS cc_start: 0.8653 (ptpt) cc_final: 0.8188 (mmtm) REVERT: B 1458 ASP cc_start: 0.8220 (m-30) cc_final: 0.7578 (t0) REVERT: B 1523 LEU cc_start: 0.7847 (mm) cc_final: 0.7568 (mt) REVERT: B 1534 CYS cc_start: 0.8640 (m) cc_final: 0.7586 (t) REVERT: B 1557 PHE cc_start: 0.7862 (m-10) cc_final: 0.7202 (m-10) REVERT: B 1578 MET cc_start: 0.7932 (tpp) cc_final: 0.7518 (tpp) REVERT: B 1631 GLU cc_start: 0.8289 (tt0) cc_final: 0.8069 (tp30) REVERT: B 1793 TRP cc_start: 0.7692 (t60) cc_final: 0.6902 (t60) REVERT: B 2274 ASP cc_start: 0.8528 (p0) cc_final: 0.7638 (p0) REVERT: B 2387 MET cc_start: 0.8720 (ptm) cc_final: 0.8461 (ptp) REVERT: C 56 MET cc_start: 0.3204 (OUTLIER) cc_final: 0.2793 (tpt) REVERT: C 65 ILE cc_start: 0.7385 (mt) cc_final: 0.7136 (mt) REVERT: C 163 GLU cc_start: 0.5751 (tt0) cc_final: 0.5257 (tm-30) REVERT: C 168 GLU cc_start: 0.6210 (pt0) cc_final: 0.5693 (pm20) REVERT: C 298 CYS cc_start: 0.7585 (t) cc_final: 0.7370 (t) REVERT: D 20 TYR cc_start: 0.7437 (m-10) cc_final: 0.7161 (m-80) REVERT: D 21 ASP cc_start: 0.7836 (t0) cc_final: 0.7626 (p0) REVERT: D 44 GLN cc_start: 0.7029 (tp-100) cc_final: 0.6430 (pm20) REVERT: D 82 ASP cc_start: 0.4672 (m-30) cc_final: 0.4126 (m-30) REVERT: D 137 HIS cc_start: 0.7918 (t-90) cc_final: 0.7289 (t-90) REVERT: D 153 HIS cc_start: 0.7039 (m90) cc_final: 0.6811 (m170) REVERT: D 163 GLU cc_start: 0.6576 (tt0) cc_final: 0.6066 (tt0) REVERT: D 168 GLU cc_start: 0.5899 (pt0) cc_final: 0.5633 (pm20) REVERT: D 198 ASN cc_start: 0.7966 (t0) cc_final: 0.7744 (t0) REVERT: D 283 GLN cc_start: 0.6972 (tm-30) cc_final: 0.6333 (mm-40) REVERT: D 307 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6931 (tm-30) REVERT: E 149 LEU cc_start: 0.8969 (tp) cc_final: 0.8716 (tp) REVERT: E 175 ASP cc_start: 0.7894 (t0) cc_final: 0.6909 (t0) REVERT: E 184 VAL cc_start: 0.8440 (m) cc_final: 0.8027 (m) REVERT: E 198 ASN cc_start: 0.9184 (t0) cc_final: 0.8897 (t0) REVERT: E 359 GLN cc_start: 0.8596 (tp40) cc_final: 0.8330 (mm-40) REVERT: E 397 SER cc_start: 0.9189 (t) cc_final: 0.8815 (p) REVERT: E 437 ILE cc_start: 0.8644 (mp) cc_final: 0.8390 (pt) REVERT: E 528 LEU cc_start: 0.8322 (tp) cc_final: 0.8100 (tp) REVERT: E 578 LEU cc_start: 0.7242 (tp) cc_final: 0.6800 (mt) REVERT: E 749 ASN cc_start: 0.7905 (m-40) cc_final: 0.7315 (m-40) REVERT: E 880 ILE cc_start: 0.8519 (mm) cc_final: 0.8236 (tp) REVERT: E 896 LEU cc_start: 0.7700 (tt) cc_final: 0.6749 (tp) REVERT: E 1432 ASP cc_start: 0.8662 (t0) cc_final: 0.8031 (t0) REVERT: E 1484 ARG cc_start: 0.6418 (tpt90) cc_final: 0.5967 (tpp-160) REVERT: E 1487 MET cc_start: 0.3608 (OUTLIER) cc_final: 0.3026 (mmm) REVERT: E 1613 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6644 (mtp180) REVERT: F 84 ILE cc_start: 0.7763 (mm) cc_final: 0.7511 (mt) REVERT: F 175 ASP cc_start: 0.7765 (t0) cc_final: 0.6622 (t0) REVERT: F 179 GLU cc_start: 0.7452 (mp0) cc_final: 0.6732 (mp0) REVERT: F 184 VAL cc_start: 0.8621 (m) cc_final: 0.8235 (m) REVERT: F 198 ASN cc_start: 0.9060 (t0) cc_final: 0.8580 (t0) REVERT: F 388 MET cc_start: 0.8104 (tpt) cc_final: 0.7662 (tpt) REVERT: F 397 SER cc_start: 0.9197 (t) cc_final: 0.8695 (p) REVERT: F 418 HIS cc_start: 0.7541 (m-70) cc_final: 0.7320 (m90) REVERT: F 569 GLN cc_start: 0.7509 (mt0) cc_final: 0.7290 (mt0) REVERT: F 578 LEU cc_start: 0.7607 (tp) cc_final: 0.7291 (mt) REVERT: F 655 LEU cc_start: 0.7851 (mp) cc_final: 0.7258 (pp) REVERT: F 702 VAL cc_start: 0.8495 (p) cc_final: 0.8251 (p) REVERT: F 749 ASN cc_start: 0.8090 (m-40) cc_final: 0.7456 (m-40) REVERT: F 880 ILE cc_start: 0.8374 (mm) cc_final: 0.8060 (mp) REVERT: F 1432 ASP cc_start: 0.8679 (t0) cc_final: 0.8123 (t0) REVERT: F 1484 ARG cc_start: 0.6473 (tpt90) cc_final: 0.5863 (tpp-160) REVERT: F 1487 MET cc_start: 0.3118 (OUTLIER) cc_final: 0.2889 (mmm) REVERT: F 1613 ARG cc_start: 0.6743 (mtp180) cc_final: 0.6495 (mtp180) REVERT: G 26 MET cc_start: 0.7110 (mmp) cc_final: 0.6891 (mmt) REVERT: H 26 MET cc_start: 0.7128 (mmp) cc_final: 0.6905 (mmt) REVERT: H 33 ASP cc_start: 0.8645 (p0) cc_final: 0.8436 (t0) REVERT: H 85 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7262 (t0) REVERT: H 108 TRP cc_start: 0.6312 (t-100) cc_final: 0.5196 (t-100) outliers start: 88 outliers final: 16 residues processed: 1996 average time/residue: 0.5735 time to fit residues: 1876.6844 Evaluate side-chains 956 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 935 time to evaluate : 5.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1487 MET Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 905 LEU Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 1487 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 88 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 628 optimal weight: 2.9990 chunk 563 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 380 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 chunk 583 optimal weight: 9.9990 chunk 225 optimal weight: 0.9980 chunk 354 optimal weight: 3.9990 chunk 434 optimal weight: 1.9990 chunk 675 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 GLN ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 HIS A1058 GLN A1112 HIS A1189 GLN A1311 ASN ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 GLN A1439 HIS A1774 GLN ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2024 HIS A2194 GLN A2206 ASN A2428 ASN B 736 GLN B 752 GLN B 759 HIS B 807 GLN B 967 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 GLN ** B1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1439 HIS ** B1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1774 GLN B1901 GLN B1959 GLN B1970 GLN B2024 HIS B2072 GLN B2189 HIS B2340 HIS ** B2410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2428 ASN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS D 128 ASN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 62 ASN E 379 HIS E 390 ASN E 447 HIS E 657 GLN E 885 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 958 GLN E1681 GLN F 61 ASN F 62 ASN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 HIS F 758 GLN F 885 GLN ** F 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 958 GLN ** F1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS H 68 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 58164 Z= 0.240 Angle : 0.716 14.653 78943 Z= 0.368 Chirality : 0.045 0.357 9158 Planarity : 0.005 0.064 10144 Dihedral : 5.731 71.047 8048 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.82 % Favored : 95.01 % Rotamer: Outliers : 3.26 % Allowed : 13.04 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 7360 helix: 0.66 (0.08), residues: 4666 sheet: -0.42 (0.28), residues: 327 loop : -1.97 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1633 HIS 0.009 0.001 HIS D 219 PHE 0.039 0.002 PHE G 78 TYR 0.027 0.002 TYR F 731 ARG 0.008 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 965 time to evaluate : 4.865 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: A 666 ASP cc_start: 0.7924 (t70) cc_final: 0.7043 (t70) REVERT: A 672 ARG cc_start: 0.6029 (mmp-170) cc_final: 0.5572 (mmt90) REVERT: A 825 MET cc_start: 0.8913 (mtp) cc_final: 0.8658 (mmm) REVERT: A 1205 ASN cc_start: 0.7130 (p0) cc_final: 0.6923 (p0) REVERT: A 1218 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7662 (mptt) REVERT: A 1282 GLU cc_start: 0.8860 (tt0) cc_final: 0.8251 (mm-30) REVERT: A 1458 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7379 (t0) REVERT: A 1466 LYS cc_start: 0.8501 (tptm) cc_final: 0.8287 (tppt) REVERT: A 1523 LEU cc_start: 0.7815 (mm) cc_final: 0.7352 (mt) REVERT: A 1638 MET cc_start: 0.8200 (tpp) cc_final: 0.7960 (ttp) REVERT: A 1649 ASP cc_start: 0.7785 (t0) cc_final: 0.6407 (p0) REVERT: A 1719 HIS cc_start: 0.8355 (t70) cc_final: 0.8002 (t-170) REVERT: A 1912 ASP cc_start: 0.6950 (t0) cc_final: 0.6665 (t70) REVERT: A 1921 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: A 1950 ARG cc_start: 0.5396 (tpp80) cc_final: 0.5077 (mmm-85) REVERT: A 2011 MET cc_start: 0.8271 (tmm) cc_final: 0.8055 (tmm) REVERT: A 2049 GLU cc_start: 0.8585 (mp0) cc_final: 0.8250 (mp0) REVERT: A 2412 ASP cc_start: 0.8438 (m-30) cc_final: 0.8173 (m-30) REVERT: A 2542 TYR cc_start: 0.7907 (t80) cc_final: 0.7593 (t80) REVERT: B 621 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7511 (tp30) REVERT: B 658 LYS cc_start: 0.9433 (mmmm) cc_final: 0.9040 (mmtp) REVERT: B 709 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7473 (mm-30) REVERT: B 811 LEU cc_start: 0.8684 (mt) cc_final: 0.8228 (mp) REVERT: B 875 GLU cc_start: 0.7696 (tp30) cc_final: 0.6513 (mt-10) REVERT: B 940 ASN cc_start: 0.8475 (t0) cc_final: 0.8197 (t0) REVERT: B 1038 MET cc_start: 0.8914 (ttm) cc_final: 0.8705 (mtm) REVERT: B 1187 LYS cc_start: 0.8336 (mttt) cc_final: 0.8000 (mmtm) REVERT: B 1362 GLU cc_start: 0.8633 (tt0) cc_final: 0.8368 (mt-10) REVERT: B 1369 LYS cc_start: 0.8676 (ptpt) cc_final: 0.8270 (mtpp) REVERT: B 1385 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8522 (tp30) REVERT: B 1458 ASP cc_start: 0.8353 (m-30) cc_final: 0.7697 (t0) REVERT: B 1487 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 1523 LEU cc_start: 0.8083 (mm) cc_final: 0.7713 (mt) REVERT: B 1534 CYS cc_start: 0.8328 (m) cc_final: 0.7297 (t) REVERT: B 1535 MET cc_start: 0.7640 (mmm) cc_final: 0.6851 (mmm) REVERT: B 1631 GLU cc_start: 0.8241 (tt0) cc_final: 0.7965 (tp30) REVERT: B 1638 MET cc_start: 0.8438 (tpp) cc_final: 0.8172 (ttp) REVERT: B 1687 HIS cc_start: 0.8035 (m90) cc_final: 0.7660 (m170) REVERT: B 2117 GLN cc_start: 0.8645 (mt0) cc_final: 0.8399 (mt0) REVERT: B 2175 MET cc_start: 0.8031 (tpp) cc_final: 0.7807 (mmm) REVERT: B 2199 MET cc_start: 0.8309 (tpt) cc_final: 0.8082 (mmm) REVERT: B 2345 MET cc_start: 0.8872 (mtp) cc_final: 0.8666 (mtm) REVERT: C 142 GLU cc_start: 0.6990 (mm-30) cc_final: 0.5346 (mp0) REVERT: C 168 GLU cc_start: 0.6359 (pt0) cc_final: 0.5799 (pm20) REVERT: D 44 GLN cc_start: 0.6878 (tp-100) cc_final: 0.6379 (pm20) REVERT: D 163 GLU cc_start: 0.6266 (tt0) cc_final: 0.5877 (pp20) REVERT: D 239 SER cc_start: 0.5650 (t) cc_final: 0.4803 (p) REVERT: D 245 LYS cc_start: 0.7462 (mttm) cc_final: 0.7223 (mmmt) REVERT: D 247 TRP cc_start: 0.5689 (m100) cc_final: 0.5451 (m100) REVERT: E 160 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8116 (tt) REVERT: E 175 ASP cc_start: 0.7887 (t0) cc_final: 0.7278 (t0) REVERT: E 179 GLU cc_start: 0.8059 (mp0) cc_final: 0.7614 (mp0) REVERT: E 198 ASN cc_start: 0.9193 (t0) cc_final: 0.8841 (t0) REVERT: E 359 GLN cc_start: 0.8604 (tp40) cc_final: 0.8364 (tp40) REVERT: E 360 ASP cc_start: 0.8157 (p0) cc_final: 0.7825 (m-30) REVERT: E 397 SER cc_start: 0.9270 (t) cc_final: 0.8812 (p) REVERT: E 749 ASN cc_start: 0.7947 (m-40) cc_final: 0.7457 (m-40) REVERT: E 791 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8063 (ptpt) REVERT: E 807 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6971 (ttp80) REVERT: E 958 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: E 968 CYS cc_start: 0.9176 (m) cc_final: 0.8792 (m) REVERT: E 998 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8334 (ttmt) REVERT: E 1432 ASP cc_start: 0.8735 (t0) cc_final: 0.8164 (t0) REVERT: E 1484 ARG cc_start: 0.6413 (tpt90) cc_final: 0.5938 (tpp-160) REVERT: E 1487 MET cc_start: 0.3563 (OUTLIER) cc_final: 0.3304 (mmm) REVERT: E 1671 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6617 (ptp-170) REVERT: F 61 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7830 (t0) REVERT: F 175 ASP cc_start: 0.7751 (t0) cc_final: 0.6594 (t0) REVERT: F 179 GLU cc_start: 0.7778 (mp0) cc_final: 0.6958 (mp0) REVERT: F 198 ASN cc_start: 0.9187 (t0) cc_final: 0.8662 (t0) REVERT: F 225 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7700 (tm-30) REVERT: F 359 GLN cc_start: 0.8480 (tp40) cc_final: 0.8249 (mm-40) REVERT: F 360 ASP cc_start: 0.8246 (p0) cc_final: 0.7840 (m-30) REVERT: F 397 SER cc_start: 0.9298 (t) cc_final: 0.8780 (p) REVERT: F 544 LEU cc_start: 0.8504 (mp) cc_final: 0.8205 (mm) REVERT: F 620 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: F 675 MET cc_start: 0.8542 (tpp) cc_final: 0.8284 (tpp) REVERT: F 694 GLN cc_start: 0.8761 (mp10) cc_final: 0.8512 (mp10) REVERT: F 749 ASN cc_start: 0.8069 (m-40) cc_final: 0.7737 (m-40) REVERT: F 880 ILE cc_start: 0.8614 (mm) cc_final: 0.8382 (mp) REVERT: F 968 CYS cc_start: 0.9085 (m) cc_final: 0.8661 (m) REVERT: F 1432 ASP cc_start: 0.8749 (t0) cc_final: 0.8221 (t0) REVERT: G 108 TRP cc_start: 0.6756 (t-100) cc_final: 0.5700 (t-100) REVERT: H 81 ARG cc_start: 0.3333 (OUTLIER) cc_final: 0.3002 (ttp-110) REVERT: H 108 TRP cc_start: 0.6009 (t-100) cc_final: 0.5365 (t-100) outliers start: 188 outliers final: 103 residues processed: 1098 average time/residue: 0.5742 time to fit residues: 1080.5935 Evaluate side-chains 858 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 743 time to evaluate : 4.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1311 ASN Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1696 VAL Chi-restraints excluded: chain A residue 1723 THR Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 2079 MET Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1287 LEU Chi-restraints excluded: chain B residue 1299 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1417 ILE Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1533 THR Chi-restraints excluded: chain B residue 1597 SER Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 1781 GLU Chi-restraints excluded: chain B residue 1805 LYS Chi-restraints excluded: chain B residue 1874 SER Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1921 GLU Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2428 ASN Chi-restraints excluded: chain B residue 2541 CYS Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 807 ARG Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 933 ILE Chi-restraints excluded: chain E residue 958 GLN Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1427 LEU Chi-restraints excluded: chain E residue 1487 MET Chi-restraints excluded: chain E residue 1631 CYS Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 620 GLN Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 933 ILE Chi-restraints excluded: chain F residue 1631 CYS Chi-restraints excluded: chain F residue 1681 GLN Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 78 PHE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 88 GLN Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 375 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 562 optimal weight: 8.9990 chunk 460 optimal weight: 0.1980 chunk 186 optimal weight: 2.9990 chunk 676 optimal weight: 10.0000 chunk 731 optimal weight: 5.9990 chunk 602 optimal weight: 0.8980 chunk 671 optimal weight: 7.9990 chunk 230 optimal weight: 50.0000 chunk 542 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 GLN A 791 ASN A 846 GLN A 967 HIS ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 GLN A1311 ASN ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1959 GLN ** B1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1183 GLN B1233 GLN B1439 HIS ** B1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1739 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 499 GLN E 547 ASN F 62 ASN F 442 HIS ** F1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58164 Z= 0.178 Angle : 0.617 12.586 78943 Z= 0.316 Chirality : 0.042 0.355 9158 Planarity : 0.004 0.057 10144 Dihedral : 4.756 74.520 8011 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.76 % Favored : 95.10 % Rotamer: Outliers : 3.09 % Allowed : 16.59 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 7360 helix: 1.05 (0.08), residues: 4638 sheet: -0.26 (0.29), residues: 329 loop : -1.83 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 247 HIS 0.007 0.001 HIS A1206 PHE 0.018 0.001 PHE A1888 TYR 0.020 0.001 TYR B2088 ARG 0.007 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 839 time to evaluate : 4.812 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: A 709 GLU cc_start: 0.7740 (tt0) cc_final: 0.7427 (mt-10) REVERT: A 1107 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 1218 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7607 (mptt) REVERT: A 1222 LEU cc_start: 0.5857 (mt) cc_final: 0.5621 (mm) REVERT: A 1225 GLU cc_start: 0.5609 (mp0) cc_final: 0.5404 (mp0) REVERT: A 1282 GLU cc_start: 0.8851 (tt0) cc_final: 0.8247 (mm-30) REVERT: A 1458 ASP cc_start: 0.7924 (m-30) cc_final: 0.7266 (t0) REVERT: A 1523 LEU cc_start: 0.7773 (mm) cc_final: 0.7322 (mt) REVERT: A 1649 ASP cc_start: 0.7990 (t0) cc_final: 0.6520 (p0) REVERT: A 1719 HIS cc_start: 0.8404 (t70) cc_final: 0.8072 (t-170) REVERT: A 1798 PHE cc_start: 0.8664 (t80) cc_final: 0.8454 (t80) REVERT: A 1921 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: A 1950 ARG cc_start: 0.5423 (tpp80) cc_final: 0.5152 (mmm-85) REVERT: A 2011 MET cc_start: 0.8327 (tmm) cc_final: 0.8064 (tmm) REVERT: A 2049 GLU cc_start: 0.8440 (mp0) cc_final: 0.8210 (mp0) REVERT: A 2134 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7645 (tpp80) REVERT: A 2412 ASP cc_start: 0.8519 (m-30) cc_final: 0.8254 (m-30) REVERT: A 2424 ASP cc_start: 0.8287 (t0) cc_final: 0.8004 (t0) REVERT: B 621 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7600 (tp30) REVERT: B 658 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9115 (mmmt) REVERT: B 701 ASN cc_start: 0.7504 (t0) cc_final: 0.7280 (t0) REVERT: B 709 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 811 LEU cc_start: 0.8658 (mt) cc_final: 0.8266 (mp) REVERT: B 863 THR cc_start: 0.9122 (p) cc_final: 0.8880 (t) REVERT: B 875 GLU cc_start: 0.7585 (tp30) cc_final: 0.6468 (mt-10) REVERT: B 940 ASN cc_start: 0.8632 (t0) cc_final: 0.8285 (t0) REVERT: B 1187 LYS cc_start: 0.8332 (mttt) cc_final: 0.8025 (mmtm) REVERT: B 1227 GLU cc_start: 0.7996 (tt0) cc_final: 0.7714 (tt0) REVERT: B 1287 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8392 (pp) REVERT: B 1369 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8263 (mtpp) REVERT: B 1385 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: B 1458 ASP cc_start: 0.8374 (m-30) cc_final: 0.7811 (t70) REVERT: B 1487 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8424 (mm) REVERT: B 1523 LEU cc_start: 0.7973 (mm) cc_final: 0.7695 (mt) REVERT: B 1534 CYS cc_start: 0.8429 (m) cc_final: 0.7361 (t) REVERT: B 1535 MET cc_start: 0.7767 (mmm) cc_final: 0.7170 (mmm) REVERT: B 1578 MET cc_start: 0.8092 (tpt) cc_final: 0.7864 (tpp) REVERT: B 1638 MET cc_start: 0.8538 (tpp) cc_final: 0.8288 (ttp) REVERT: B 1687 HIS cc_start: 0.7889 (m90) cc_final: 0.7616 (m90) REVERT: B 1952 LEU cc_start: 0.8367 (mt) cc_final: 0.8130 (mt) REVERT: B 2059 GLU cc_start: 0.8662 (tp30) cc_final: 0.8365 (tp30) REVERT: B 2175 MET cc_start: 0.8714 (tpp) cc_final: 0.8498 (tpp) REVERT: B 2404 MET cc_start: 0.8434 (mmm) cc_final: 0.8160 (tpt) REVERT: C 142 GLU cc_start: 0.7002 (mm-30) cc_final: 0.5511 (mp0) REVERT: D 44 GLN cc_start: 0.6783 (tp-100) cc_final: 0.6294 (pm20) REVERT: D 163 GLU cc_start: 0.6589 (tt0) cc_final: 0.6089 (tm-30) REVERT: D 239 SER cc_start: 0.4935 (t) cc_final: 0.4123 (p) REVERT: E 160 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8081 (tt) REVERT: E 175 ASP cc_start: 0.8004 (t0) cc_final: 0.7354 (t0) REVERT: E 198 ASN cc_start: 0.9227 (t0) cc_final: 0.8806 (t0) REVERT: E 360 ASP cc_start: 0.8181 (p0) cc_final: 0.7923 (m-30) REVERT: E 397 SER cc_start: 0.9284 (t) cc_final: 0.8787 (p) REVERT: E 749 ASN cc_start: 0.8130 (m-40) cc_final: 0.7758 (m-40) REVERT: E 791 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8084 (ptpt) REVERT: E 958 GLN cc_start: 0.7398 (mm110) cc_final: 0.6987 (mt0) REVERT: E 968 CYS cc_start: 0.9260 (m) cc_final: 0.8811 (m) REVERT: E 1432 ASP cc_start: 0.8726 (t0) cc_final: 0.8173 (t0) REVERT: E 1607 MET cc_start: 0.5397 (mmp) cc_final: 0.5082 (mmp) REVERT: F 122 LYS cc_start: 0.7842 (ptpp) cc_final: 0.7616 (tttp) REVERT: F 175 ASP cc_start: 0.7822 (t0) cc_final: 0.7469 (t0) REVERT: F 179 GLU cc_start: 0.7923 (mp0) cc_final: 0.7583 (mp0) REVERT: F 198 ASN cc_start: 0.9232 (t0) cc_final: 0.8715 (t0) REVERT: F 254 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7606 (pp) REVERT: F 359 GLN cc_start: 0.8502 (tp40) cc_final: 0.8282 (mm-40) REVERT: F 360 ASP cc_start: 0.8280 (p0) cc_final: 0.7856 (m-30) REVERT: F 397 SER cc_start: 0.9321 (t) cc_final: 0.8788 (p) REVERT: F 482 MET cc_start: 0.8849 (tmm) cc_final: 0.8594 (tmm) REVERT: F 694 GLN cc_start: 0.8811 (mp10) cc_final: 0.8536 (mp10) REVERT: F 749 ASN cc_start: 0.8148 (m-40) cc_final: 0.7790 (m-40) REVERT: F 968 CYS cc_start: 0.9019 (m) cc_final: 0.8515 (m) REVERT: F 1432 ASP cc_start: 0.8740 (t0) cc_final: 0.8218 (t0) REVERT: F 1484 ARG cc_start: 0.6277 (ptt180) cc_final: 0.5425 (tpp-160) REVERT: F 1655 GLU cc_start: 0.8383 (tt0) cc_final: 0.8175 (tt0) REVERT: F 1671 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7619 (ttp80) REVERT: H 108 TRP cc_start: 0.5959 (t-100) cc_final: 0.5197 (t-100) outliers start: 178 outliers final: 109 residues processed: 965 average time/residue: 0.4982 time to fit residues: 831.3928 Evaluate side-chains 831 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 714 time to evaluate : 4.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 967 HIS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1696 VAL Chi-restraints excluded: chain A residue 1723 THR Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 2005 LEU Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1287 LEU Chi-restraints excluded: chain B residue 1299 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1417 ILE Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1533 THR Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 1781 GLU Chi-restraints excluded: chain B residue 1805 LYS Chi-restraints excluded: chain B residue 1874 SER Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1960 LEU Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2246 LEU Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2541 CYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 933 ILE Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1427 LEU Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 933 ILE Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 668 optimal weight: 2.9990 chunk 508 optimal weight: 0.9990 chunk 351 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 chunk 454 optimal weight: 20.0000 chunk 679 optimal weight: 6.9990 chunk 719 optimal weight: 0.0370 chunk 354 optimal weight: 0.9990 chunk 643 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A 966 HIS A1206 HIS ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1634 GLN A1687 HIS ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 HIS A2537 ASN B 846 GLN ** B1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1901 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN E 442 HIS E 547 ASN E 958 GLN F 264 HIS F 442 HIS F1681 GLN ** F1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 58164 Z= 0.193 Angle : 0.597 13.706 78943 Z= 0.304 Chirality : 0.041 0.338 9158 Planarity : 0.004 0.052 10144 Dihedral : 4.320 25.366 8002 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.55 % Favored : 95.34 % Rotamer: Outliers : 3.42 % Allowed : 18.17 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7360 helix: 1.24 (0.08), residues: 4641 sheet: -0.27 (0.28), residues: 334 loop : -1.76 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1521 HIS 0.012 0.001 HIS A 967 PHE 0.030 0.001 PHE B 705 TYR 0.023 0.001 TYR A1393 ARG 0.011 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 751 time to evaluate : 4.860 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: A 727 MET cc_start: 0.8279 (tpt) cc_final: 0.7980 (mmm) REVERT: A 994 MET cc_start: 0.9251 (tpt) cc_final: 0.9018 (tpt) REVERT: A 1107 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8423 (pp) REVERT: A 1218 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7540 (mptt) REVERT: A 1225 GLU cc_start: 0.5817 (mp0) cc_final: 0.5592 (mp0) REVERT: A 1282 GLU cc_start: 0.8825 (tt0) cc_final: 0.8141 (mm-30) REVERT: A 1458 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7277 (t0) REVERT: A 1523 LEU cc_start: 0.7864 (mm) cc_final: 0.7442 (mt) REVERT: A 1649 ASP cc_start: 0.8098 (t0) cc_final: 0.6548 (p0) REVERT: A 1719 HIS cc_start: 0.8467 (t70) cc_final: 0.8135 (t-170) REVERT: A 1724 MET cc_start: 0.8898 (mmm) cc_final: 0.8646 (tpp) REVERT: A 1921 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8689 (mp0) REVERT: A 1988 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.7020 (p-80) REVERT: A 2011 MET cc_start: 0.8405 (tmm) cc_final: 0.8123 (tmm) REVERT: A 2338 ASP cc_start: 0.7796 (t70) cc_final: 0.7157 (t0) REVERT: A 2409 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 2412 ASP cc_start: 0.8451 (m-30) cc_final: 0.8236 (m-30) REVERT: B 621 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7602 (tp30) REVERT: B 811 LEU cc_start: 0.8583 (mt) cc_final: 0.8258 (mp) REVERT: B 940 ASN cc_start: 0.8719 (t0) cc_final: 0.8373 (t0) REVERT: B 1187 LYS cc_start: 0.8419 (mttt) cc_final: 0.8136 (mmtm) REVERT: B 1224 ASP cc_start: 0.7170 (t70) cc_final: 0.6855 (t0) REVERT: B 1226 GLU cc_start: 0.7264 (tt0) cc_final: 0.6985 (tp30) REVERT: B 1369 LYS cc_start: 0.8767 (ptpt) cc_final: 0.8323 (mtpp) REVERT: B 1385 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8357 (tp30) REVERT: B 1458 ASP cc_start: 0.8455 (m-30) cc_final: 0.7738 (t0) REVERT: B 1487 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8438 (mm) REVERT: B 1523 LEU cc_start: 0.7985 (mm) cc_final: 0.7632 (mt) REVERT: B 1638 MET cc_start: 0.8511 (tpp) cc_final: 0.8257 (ttp) REVERT: B 1687 HIS cc_start: 0.7893 (m90) cc_final: 0.7668 (m170) REVERT: B 1719 HIS cc_start: 0.8201 (t70) cc_final: 0.7730 (t-170) REVERT: B 1742 GLU cc_start: 0.6799 (mp0) cc_final: 0.6373 (mp0) REVERT: B 1959 GLN cc_start: 0.8884 (mp10) cc_final: 0.8649 (mt0) REVERT: B 1988 HIS cc_start: 0.7775 (p-80) cc_final: 0.7233 (p-80) REVERT: B 2155 SER cc_start: 0.8816 (t) cc_final: 0.8553 (p) REVERT: B 2175 MET cc_start: 0.8705 (tpp) cc_final: 0.8408 (tpp) REVERT: B 2338 ASP cc_start: 0.8019 (t0) cc_final: 0.7573 (t70) REVERT: B 2404 MET cc_start: 0.8435 (mmm) cc_final: 0.8107 (tpt) REVERT: C 49 GLU cc_start: 0.7628 (mp0) cc_final: 0.7381 (mp0) REVERT: D 239 SER cc_start: 0.4329 (t) cc_final: 0.3940 (p) REVERT: E 153 MET cc_start: 0.8880 (mtp) cc_final: 0.8676 (mtm) REVERT: E 175 ASP cc_start: 0.8157 (t0) cc_final: 0.7448 (t0) REVERT: E 198 ASN cc_start: 0.9304 (t0) cc_final: 0.8811 (t0) REVERT: E 254 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7755 (pp) REVERT: E 360 ASP cc_start: 0.8249 (p0) cc_final: 0.7949 (m-30) REVERT: E 397 SER cc_start: 0.9305 (t) cc_final: 0.8798 (p) REVERT: E 749 ASN cc_start: 0.8172 (m-40) cc_final: 0.7797 (m-40) REVERT: E 958 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7077 (mt0) REVERT: E 968 CYS cc_start: 0.9245 (m) cc_final: 0.8721 (m) REVERT: E 972 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8815 (tp) REVERT: E 1432 ASP cc_start: 0.8729 (t0) cc_final: 0.8182 (t0) REVERT: E 1607 MET cc_start: 0.5497 (mmp) cc_final: 0.5117 (mmp) REVERT: E 1622 ASN cc_start: 0.8434 (t0) cc_final: 0.8123 (m-40) REVERT: F 175 ASP cc_start: 0.7936 (t0) cc_final: 0.7286 (t0) REVERT: F 198 ASN cc_start: 0.9261 (t0) cc_final: 0.8765 (t0) REVERT: F 225 GLU cc_start: 0.8393 (tp30) cc_final: 0.8083 (tp30) REVERT: F 254 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7718 (pp) REVERT: F 359 GLN cc_start: 0.8537 (tp40) cc_final: 0.8302 (mm-40) REVERT: F 360 ASP cc_start: 0.8218 (p0) cc_final: 0.7842 (m-30) REVERT: F 397 SER cc_start: 0.9353 (t) cc_final: 0.8822 (p) REVERT: F 544 LEU cc_start: 0.8571 (mp) cc_final: 0.8293 (mm) REVERT: F 749 ASN cc_start: 0.8159 (m-40) cc_final: 0.7948 (m-40) REVERT: F 968 CYS cc_start: 0.8998 (m) cc_final: 0.8497 (m) REVERT: F 1432 ASP cc_start: 0.8762 (t0) cc_final: 0.8228 (t0) REVERT: F 1484 ARG cc_start: 0.6401 (ptt180) cc_final: 0.5416 (tpp-160) REVERT: F 1655 GLU cc_start: 0.8370 (tt0) cc_final: 0.8125 (tt0) REVERT: F 1671 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7589 (ttp80) REVERT: F 1681 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: H 66 TYR cc_start: 0.5841 (OUTLIER) cc_final: 0.5465 (m-80) REVERT: H 108 TRP cc_start: 0.5850 (t-100) cc_final: 0.4995 (t-100) outliers start: 197 outliers final: 131 residues processed: 890 average time/residue: 0.5040 time to fit residues: 778.9572 Evaluate side-chains 823 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 680 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1696 VAL Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2274 ASP Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2318 THR Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain A residue 2428 ASN Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1299 SER Chi-restraints excluded: chain B residue 1347 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1533 THR Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 1781 GLU Chi-restraints excluded: chain B residue 1874 SER Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2222 ILE Chi-restraints excluded: chain B residue 2250 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 TRP Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 667 SER Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 933 ILE Chi-restraints excluded: chain E residue 958 GLN Chi-restraints excluded: chain E residue 972 LEU Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 921 LYS Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1631 CYS Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain F residue 1681 GLN Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 598 optimal weight: 0.7980 chunk 408 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 535 optimal weight: 0.9990 chunk 296 optimal weight: 8.9990 chunk 613 optimal weight: 10.0000 chunk 497 optimal weight: 8.9990 chunk 0 optimal weight: 70.0000 chunk 367 optimal weight: 2.9990 chunk 645 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 GLN A1333 GLN A1687 HIS A2117 GLN ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1901 GLN ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 HIS E 547 ASN F 390 ASN F 435 ASN F 442 HIS ** F1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 58164 Z= 0.166 Angle : 0.577 14.720 78943 Z= 0.291 Chirality : 0.040 0.339 9158 Planarity : 0.004 0.050 10144 Dihedral : 4.166 24.049 8001 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 3.45 % Allowed : 19.33 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 7360 helix: 1.37 (0.08), residues: 4653 sheet: -0.28 (0.28), residues: 334 loop : -1.75 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1456 HIS 0.008 0.001 HIS A 966 PHE 0.034 0.001 PHE B 705 TYR 0.017 0.001 TYR B2088 ARG 0.007 0.000 ARG E 576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 745 time to evaluate : 5.030 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: A 709 GLU cc_start: 0.7811 (tt0) cc_final: 0.7560 (mt-10) REVERT: A 807 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: A 1107 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8369 (pp) REVERT: A 1141 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7999 (ttm-80) REVERT: A 1208 ARG cc_start: 0.7591 (ptm160) cc_final: 0.7301 (ttp80) REVERT: A 1225 GLU cc_start: 0.5789 (mp0) cc_final: 0.5568 (mp0) REVERT: A 1282 GLU cc_start: 0.8777 (tt0) cc_final: 0.8088 (mm-30) REVERT: A 1458 ASP cc_start: 0.8011 (m-30) cc_final: 0.7272 (t0) REVERT: A 1523 LEU cc_start: 0.7851 (mm) cc_final: 0.7469 (mt) REVERT: A 1649 ASP cc_start: 0.8127 (t0) cc_final: 0.6722 (p0) REVERT: A 1719 HIS cc_start: 0.8452 (t70) cc_final: 0.8132 (t-170) REVERT: A 1724 MET cc_start: 0.8669 (mmm) cc_final: 0.8468 (tpt) REVERT: A 1921 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8649 (mp0) REVERT: A 1988 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.6971 (p-80) REVERT: A 2011 MET cc_start: 0.8443 (tmm) cc_final: 0.8179 (tmm) REVERT: A 2049 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8296 (mp0) REVERT: A 2338 ASP cc_start: 0.7863 (t70) cc_final: 0.7218 (t0) REVERT: A 2409 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 2424 ASP cc_start: 0.8437 (t0) cc_final: 0.8095 (t0) REVERT: B 621 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7612 (tp30) REVERT: B 811 LEU cc_start: 0.8502 (mt) cc_final: 0.8215 (mp) REVERT: B 863 THR cc_start: 0.9126 (p) cc_final: 0.8831 (t) REVERT: B 940 ASN cc_start: 0.8721 (t0) cc_final: 0.8477 (t0) REVERT: B 1269 TRP cc_start: 0.6373 (m100) cc_final: 0.5568 (m100) REVERT: B 1369 LYS cc_start: 0.8786 (ptpt) cc_final: 0.8354 (mtpp) REVERT: B 1385 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8406 (tp30) REVERT: B 1458 ASP cc_start: 0.8412 (m-30) cc_final: 0.7707 (t0) REVERT: B 1474 PRO cc_start: 0.8031 (Cg_exo) cc_final: 0.7543 (Cg_endo) REVERT: B 1487 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 1523 LEU cc_start: 0.7991 (mm) cc_final: 0.7621 (mt) REVERT: B 1638 MET cc_start: 0.8528 (tpp) cc_final: 0.8255 (ttp) REVERT: B 1687 HIS cc_start: 0.7900 (m90) cc_final: 0.7675 (m170) REVERT: B 1719 HIS cc_start: 0.8231 (t70) cc_final: 0.7754 (t-170) REVERT: B 1921 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8850 (mp0) REVERT: B 1924 VAL cc_start: 0.8469 (t) cc_final: 0.8267 (t) REVERT: B 1959 GLN cc_start: 0.8889 (mp10) cc_final: 0.8618 (mt0) REVERT: B 1988 HIS cc_start: 0.7763 (p-80) cc_final: 0.7140 (p-80) REVERT: B 2155 SER cc_start: 0.8808 (t) cc_final: 0.8560 (p) REVERT: B 2338 ASP cc_start: 0.8057 (t0) cc_final: 0.7535 (t70) REVERT: B 2415 MET cc_start: 0.7694 (tpp) cc_final: 0.7321 (ttt) REVERT: D 102 THR cc_start: 0.7279 (OUTLIER) cc_final: 0.7076 (p) REVERT: D 239 SER cc_start: 0.4397 (t) cc_final: 0.3945 (p) REVERT: E 160 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8070 (tt) REVERT: E 175 ASP cc_start: 0.8210 (t0) cc_final: 0.7483 (t0) REVERT: E 198 ASN cc_start: 0.9309 (t0) cc_final: 0.8854 (t0) REVERT: E 254 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7772 (pp) REVERT: E 359 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: E 360 ASP cc_start: 0.8261 (p0) cc_final: 0.7990 (m-30) REVERT: E 397 SER cc_start: 0.9359 (t) cc_final: 0.8844 (p) REVERT: E 749 ASN cc_start: 0.8178 (m-40) cc_final: 0.7802 (m-40) REVERT: E 958 GLN cc_start: 0.7433 (mm110) cc_final: 0.6994 (mt0) REVERT: E 968 CYS cc_start: 0.9253 (m) cc_final: 0.8750 (m) REVERT: E 998 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8291 (tppt) REVERT: E 1432 ASP cc_start: 0.8730 (t0) cc_final: 0.8267 (t0) REVERT: E 1607 MET cc_start: 0.5774 (mmp) cc_final: 0.5401 (mmp) REVERT: E 1622 ASN cc_start: 0.8429 (t0) cc_final: 0.8129 (m-40) REVERT: E 1671 ARG cc_start: 0.7590 (ptp90) cc_final: 0.7102 (ttp80) REVERT: F 175 ASP cc_start: 0.8037 (t0) cc_final: 0.7329 (t0) REVERT: F 198 ASN cc_start: 0.9256 (t0) cc_final: 0.8800 (t0) REVERT: F 225 GLU cc_start: 0.8353 (tp30) cc_final: 0.7926 (tp30) REVERT: F 254 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7693 (pp) REVERT: F 359 GLN cc_start: 0.8546 (tp40) cc_final: 0.8317 (mm-40) REVERT: F 360 ASP cc_start: 0.8278 (p0) cc_final: 0.7898 (m-30) REVERT: F 397 SER cc_start: 0.9358 (t) cc_final: 0.8827 (p) REVERT: F 544 LEU cc_start: 0.8585 (mp) cc_final: 0.8306 (mm) REVERT: F 749 ASN cc_start: 0.8171 (m-40) cc_final: 0.7959 (m-40) REVERT: F 968 CYS cc_start: 0.9019 (m) cc_final: 0.8545 (m) REVERT: F 998 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8585 (mtmt) REVERT: F 1432 ASP cc_start: 0.8749 (t0) cc_final: 0.8258 (t0) REVERT: F 1484 ARG cc_start: 0.6399 (ptt180) cc_final: 0.5403 (tpp-160) REVERT: F 1655 GLU cc_start: 0.8368 (tt0) cc_final: 0.8070 (tt0) REVERT: G 108 TRP cc_start: 0.6963 (t-100) cc_final: 0.5859 (t-100) REVERT: H 66 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: H 108 TRP cc_start: 0.6192 (t-100) cc_final: 0.5298 (t-100) outliers start: 199 outliers final: 132 residues processed: 890 average time/residue: 0.4973 time to fit residues: 775.7609 Evaluate side-chains 819 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 674 time to evaluate : 4.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1141 ARG Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1756 GLU Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1902 ASP Chi-restraints excluded: chain A residue 1903 THR Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2274 ASP Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2428 ASN Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1299 SER Chi-restraints excluded: chain B residue 1347 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1533 THR Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 1781 GLU Chi-restraints excluded: chain B residue 1805 LYS Chi-restraints excluded: chain B residue 1874 SER Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2222 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2419 GLU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 TRP Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 359 GLN Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 933 ILE Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 435 ASN Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 921 LYS Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1427 LEU Chi-restraints excluded: chain F residue 1631 CYS Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 241 optimal weight: 80.0000 chunk 647 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 422 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 719 optimal weight: 0.0770 chunk 597 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 377 optimal weight: 0.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 GLN A 966 HIS A1687 HIS ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1233 GLN ** B1334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1425 GLN ** B1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1901 GLN B1920 ASN B2117 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 58164 Z= 0.159 Angle : 0.570 16.280 78943 Z= 0.286 Chirality : 0.040 0.335 9158 Planarity : 0.004 0.092 10144 Dihedral : 4.046 24.169 8001 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 3.35 % Allowed : 20.17 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.10), residues: 7360 helix: 1.43 (0.08), residues: 4666 sheet: -0.28 (0.28), residues: 334 loop : -1.75 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 297 HIS 0.006 0.001 HIS B2410 PHE 0.038 0.001 PHE B 705 TYR 0.017 0.001 TYR B1232 ARG 0.015 0.000 ARG A2430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 717 time to evaluate : 4.962 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: A 703 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: A 709 GLU cc_start: 0.7769 (tt0) cc_final: 0.7422 (mt-10) REVERT: A 733 MET cc_start: 0.7543 (mmm) cc_final: 0.7315 (mmm) REVERT: A 807 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: A 1107 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8376 (pp) REVERT: A 1141 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8030 (ttm-80) REVERT: A 1282 GLU cc_start: 0.8758 (tt0) cc_final: 0.8064 (mm-30) REVERT: A 1458 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7260 (t0) REVERT: A 1487 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 1523 LEU cc_start: 0.7869 (mm) cc_final: 0.7511 (mt) REVERT: A 1649 ASP cc_start: 0.8161 (t0) cc_final: 0.6724 (p0) REVERT: A 1719 HIS cc_start: 0.8492 (t70) cc_final: 0.8180 (t-170) REVERT: A 1921 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8702 (mp0) REVERT: A 1988 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6937 (p-80) REVERT: A 2011 MET cc_start: 0.8471 (tmm) cc_final: 0.8200 (tmm) REVERT: A 2338 ASP cc_start: 0.8023 (t70) cc_final: 0.7375 (t0) REVERT: A 2382 MET cc_start: 0.8527 (tpp) cc_final: 0.8325 (tpp) REVERT: A 2409 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 2424 ASP cc_start: 0.8375 (t0) cc_final: 0.8043 (t0) REVERT: B 621 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7594 (tp30) REVERT: B 658 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9090 (mttt) REVERT: B 811 LEU cc_start: 0.8552 (mt) cc_final: 0.8280 (mp) REVERT: B 825 MET cc_start: 0.8608 (ttp) cc_final: 0.8296 (mmm) REVERT: B 838 GLN cc_start: 0.7659 (tt0) cc_final: 0.7175 (tp40) REVERT: B 940 ASN cc_start: 0.8750 (t0) cc_final: 0.8550 (t0) REVERT: B 1140 ASP cc_start: 0.7293 (t0) cc_final: 0.6998 (t0) REVERT: B 1269 TRP cc_start: 0.6467 (m100) cc_final: 0.5466 (m100) REVERT: B 1299 SER cc_start: 0.8417 (p) cc_final: 0.8092 (t) REVERT: B 1369 LYS cc_start: 0.8790 (ptpt) cc_final: 0.8410 (mmtt) REVERT: B 1385 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8395 (tp30) REVERT: B 1421 ASN cc_start: 0.8642 (t0) cc_final: 0.8359 (t0) REVERT: B 1458 ASP cc_start: 0.8367 (m-30) cc_final: 0.7681 (t0) REVERT: B 1687 HIS cc_start: 0.7902 (m90) cc_final: 0.7681 (m170) REVERT: B 1719 HIS cc_start: 0.8253 (t70) cc_final: 0.7786 (t-170) REVERT: B 1921 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8681 (mp0) REVERT: B 1988 HIS cc_start: 0.7719 (p-80) cc_final: 0.7003 (p-80) REVERT: B 2155 SER cc_start: 0.8810 (t) cc_final: 0.8577 (p) REVERT: B 2338 ASP cc_start: 0.8116 (t0) cc_final: 0.7627 (t70) REVERT: B 2415 MET cc_start: 0.7661 (tpp) cc_final: 0.7379 (ttt) REVERT: C 273 MET cc_start: 0.8593 (tpp) cc_final: 0.7591 (mmt) REVERT: D 239 SER cc_start: 0.4451 (t) cc_final: 0.4138 (p) REVERT: E 76 LYS cc_start: 0.7749 (ttpt) cc_final: 0.7328 (ptmt) REVERT: E 160 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8094 (tt) REVERT: E 175 ASP cc_start: 0.8265 (t0) cc_final: 0.7564 (t0) REVERT: E 198 ASN cc_start: 0.9315 (t0) cc_final: 0.8882 (t0) REVERT: E 254 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7775 (pp) REVERT: E 360 ASP cc_start: 0.8222 (p0) cc_final: 0.7994 (m-30) REVERT: E 397 SER cc_start: 0.9355 (t) cc_final: 0.8840 (p) REVERT: E 749 ASN cc_start: 0.8154 (m-40) cc_final: 0.7770 (m-40) REVERT: E 958 GLN cc_start: 0.7443 (mm110) cc_final: 0.6922 (mt0) REVERT: E 968 CYS cc_start: 0.9233 (m) cc_final: 0.8756 (m) REVERT: E 1432 ASP cc_start: 0.8722 (t0) cc_final: 0.8277 (t0) REVERT: E 1607 MET cc_start: 0.5766 (mmp) cc_final: 0.5416 (mmm) REVERT: E 1671 ARG cc_start: 0.7588 (ptp90) cc_final: 0.7121 (ttp80) REVERT: F 153 MET cc_start: 0.8939 (mtm) cc_final: 0.8624 (mtt) REVERT: F 175 ASP cc_start: 0.8200 (t0) cc_final: 0.7481 (t0) REVERT: F 187 CYS cc_start: 0.9172 (m) cc_final: 0.8955 (m) REVERT: F 198 ASN cc_start: 0.9347 (t0) cc_final: 0.8892 (t0) REVERT: F 254 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7721 (pp) REVERT: F 359 GLN cc_start: 0.8528 (tp40) cc_final: 0.8310 (mm-40) REVERT: F 360 ASP cc_start: 0.8284 (p0) cc_final: 0.7932 (m-30) REVERT: F 397 SER cc_start: 0.9367 (t) cc_final: 0.8825 (p) REVERT: F 544 LEU cc_start: 0.8574 (mp) cc_final: 0.8301 (mm) REVERT: F 749 ASN cc_start: 0.8180 (m-40) cc_final: 0.7968 (m-40) REVERT: F 968 CYS cc_start: 0.9028 (m) cc_final: 0.8575 (m) REVERT: F 998 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8575 (mtmt) REVERT: F 1432 ASP cc_start: 0.8707 (t0) cc_final: 0.8190 (t0) REVERT: F 1484 ARG cc_start: 0.6395 (ptt180) cc_final: 0.5406 (tpp-160) REVERT: F 1655 GLU cc_start: 0.8442 (tt0) cc_final: 0.8130 (tt0) REVERT: F 1671 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7669 (ttp80) REVERT: H 108 TRP cc_start: 0.6289 (t-100) cc_final: 0.5420 (t-100) outliers start: 193 outliers final: 133 residues processed: 861 average time/residue: 0.5051 time to fit residues: 759.5966 Evaluate side-chains 815 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 670 time to evaluate : 4.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1141 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1638 MET Chi-restraints excluded: chain A residue 1756 GLU Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1902 ASP Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2274 ASP Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2428 ASN Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1081 VAL Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1194 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1347 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1590 MET Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 1781 GLU Chi-restraints excluded: chain B residue 1805 LYS Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2222 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2541 CYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 TRP Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1427 LEU Chi-restraints excluded: chain F residue 1631 CYS Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 694 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 410 optimal weight: 0.7980 chunk 525 optimal weight: 0.9990 chunk 407 optimal weight: 0.7980 chunk 605 optimal weight: 5.9990 chunk 401 optimal weight: 0.0670 chunk 717 optimal weight: 0.9990 chunk 448 optimal weight: 8.9990 chunk 437 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 GLN A1553 HIS A1687 HIS A2194 GLN ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1334 GLN B1366 HIS B1729 GLN B1901 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN E 758 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 908 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 58164 Z= 0.148 Angle : 0.563 14.138 78943 Z= 0.282 Chirality : 0.040 0.339 9158 Planarity : 0.004 0.084 10144 Dihedral : 3.934 23.664 8001 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 3.07 % Allowed : 21.03 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.10), residues: 7360 helix: 1.49 (0.08), residues: 4656 sheet: -0.20 (0.28), residues: 342 loop : -1.70 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 297 HIS 0.005 0.000 HIS A1594 PHE 0.040 0.001 PHE B 705 TYR 0.017 0.001 TYR B1220 ARG 0.021 0.000 ARG A2430 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 734 time to evaluate : 4.864 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: A 733 MET cc_start: 0.7542 (mmm) cc_final: 0.7286 (mmm) REVERT: A 807 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: A 940 ASN cc_start: 0.8550 (t0) cc_final: 0.8215 (t0) REVERT: A 1107 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8334 (pp) REVERT: A 1141 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8035 (ttm-80) REVERT: A 1203 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.7641 (ptp90) REVERT: A 1225 GLU cc_start: 0.5609 (mp0) cc_final: 0.5367 (mp0) REVERT: A 1282 GLU cc_start: 0.8763 (tt0) cc_final: 0.8094 (mm-30) REVERT: A 1458 ASP cc_start: 0.8008 (m-30) cc_final: 0.7257 (t0) REVERT: A 1487 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 1523 LEU cc_start: 0.7855 (mm) cc_final: 0.7535 (mt) REVERT: A 1649 ASP cc_start: 0.8175 (t0) cc_final: 0.6820 (p0) REVERT: A 1719 HIS cc_start: 0.8485 (t70) cc_final: 0.8163 (t-170) REVERT: A 1724 MET cc_start: 0.9170 (tpp) cc_final: 0.8918 (tpp) REVERT: A 1921 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8622 (mp0) REVERT: A 1988 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6888 (p-80) REVERT: A 2011 MET cc_start: 0.8518 (tmm) cc_final: 0.8253 (tmm) REVERT: A 2338 ASP cc_start: 0.8054 (t70) cc_final: 0.7431 (t0) REVERT: A 2382 MET cc_start: 0.8520 (tpp) cc_final: 0.8295 (tpp) REVERT: A 2409 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 2424 ASP cc_start: 0.8309 (t0) cc_final: 0.7994 (t0) REVERT: B 621 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7636 (tp30) REVERT: B 658 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9090 (mttt) REVERT: B 811 LEU cc_start: 0.8552 (mt) cc_final: 0.8267 (mp) REVERT: B 825 MET cc_start: 0.8616 (ttp) cc_final: 0.8351 (mmm) REVERT: B 838 GLN cc_start: 0.7660 (tt0) cc_final: 0.7150 (tp40) REVERT: B 1140 ASP cc_start: 0.7296 (t0) cc_final: 0.7077 (t0) REVERT: B 1269 TRP cc_start: 0.6389 (m100) cc_final: 0.5273 (m100) REVERT: B 1299 SER cc_start: 0.8392 (p) cc_final: 0.8050 (t) REVERT: B 1385 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: B 1421 ASN cc_start: 0.8611 (t0) cc_final: 0.8341 (t0) REVERT: B 1458 ASP cc_start: 0.8292 (m-30) cc_final: 0.7623 (t0) REVERT: B 1487 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8429 (mm) REVERT: B 1523 LEU cc_start: 0.7955 (mm) cc_final: 0.7549 (mt) REVERT: B 1687 HIS cc_start: 0.7820 (m90) cc_final: 0.7617 (m170) REVERT: B 1719 HIS cc_start: 0.8268 (t70) cc_final: 0.7789 (t-170) REVERT: B 1921 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8695 (mt-10) REVERT: B 1988 HIS cc_start: 0.7698 (p-80) cc_final: 0.6953 (p-80) REVERT: B 2155 SER cc_start: 0.8802 (t) cc_final: 0.8572 (p) REVERT: B 2329 MET cc_start: 0.8425 (tpp) cc_final: 0.8144 (tpp) REVERT: B 2338 ASP cc_start: 0.8120 (t0) cc_final: 0.7641 (t70) REVERT: B 2415 MET cc_start: 0.7637 (tpp) cc_final: 0.7396 (ttt) REVERT: C 101 TYR cc_start: 0.6961 (p90) cc_final: 0.6732 (p90) REVERT: C 142 GLU cc_start: 0.7262 (mm-30) cc_final: 0.5655 (mp0) REVERT: D 101 TYR cc_start: 0.7083 (p90) cc_final: 0.6777 (p90) REVERT: D 247 TRP cc_start: 0.6167 (OUTLIER) cc_final: 0.5876 (m100) REVERT: E 175 ASP cc_start: 0.8309 (t0) cc_final: 0.7563 (t0) REVERT: E 198 ASN cc_start: 0.9332 (t0) cc_final: 0.8942 (t0) REVERT: E 254 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7796 (pp) REVERT: E 397 SER cc_start: 0.9348 (t) cc_final: 0.8822 (p) REVERT: E 749 ASN cc_start: 0.8140 (m-40) cc_final: 0.7754 (m-40) REVERT: E 806 LEU cc_start: 0.9181 (tp) cc_final: 0.8973 (tt) REVERT: E 958 GLN cc_start: 0.7369 (mm110) cc_final: 0.6851 (mt0) REVERT: E 968 CYS cc_start: 0.9210 (m) cc_final: 0.8745 (m) REVERT: E 1432 ASP cc_start: 0.8646 (t0) cc_final: 0.8197 (t0) REVERT: E 1484 ARG cc_start: 0.6528 (tpt90) cc_final: 0.5947 (tpp-160) REVERT: E 1607 MET cc_start: 0.5700 (mmp) cc_final: 0.5366 (mmm) REVERT: F 175 ASP cc_start: 0.8217 (t0) cc_final: 0.7486 (t0) REVERT: F 198 ASN cc_start: 0.9348 (t0) cc_final: 0.8981 (t0) REVERT: F 254 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7622 (pp) REVERT: F 359 GLN cc_start: 0.8545 (tp40) cc_final: 0.8320 (mm-40) REVERT: F 360 ASP cc_start: 0.8287 (p0) cc_final: 0.7974 (m-30) REVERT: F 397 SER cc_start: 0.9368 (t) cc_final: 0.8796 (p) REVERT: F 544 LEU cc_start: 0.8538 (mp) cc_final: 0.8267 (mm) REVERT: F 749 ASN cc_start: 0.8179 (m-40) cc_final: 0.7967 (m-40) REVERT: F 797 LEU cc_start: 0.8628 (mt) cc_final: 0.8347 (mp) REVERT: F 968 CYS cc_start: 0.9047 (m) cc_final: 0.8616 (m) REVERT: F 998 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8559 (mtmt) REVERT: F 1432 ASP cc_start: 0.8675 (t0) cc_final: 0.8164 (t0) REVERT: F 1484 ARG cc_start: 0.6347 (ptt180) cc_final: 0.5405 (tpp-160) REVERT: F 1671 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7641 (ttp80) REVERT: H 108 TRP cc_start: 0.6400 (t-100) cc_final: 0.5503 (t-100) outliers start: 177 outliers final: 129 residues processed: 866 average time/residue: 0.5057 time to fit residues: 761.9556 Evaluate side-chains 817 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 677 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1082 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1141 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1638 MET Chi-restraints excluded: chain A residue 1675 LEU Chi-restraints excluded: chain A residue 1756 GLU Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1902 ASP Chi-restraints excluded: chain A residue 1903 THR Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2274 ASP Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2428 ASN Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1122 PHE Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1194 MET Chi-restraints excluded: chain B residue 1347 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1590 MET Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1781 GLU Chi-restraints excluded: chain B residue 1805 LYS Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2222 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2419 GLU Chi-restraints excluded: chain B residue 2541 CYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 TRP Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1427 LEU Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 591 LEU Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1427 LEU Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 443 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 428 optimal weight: 1.9990 chunk 216 optimal weight: 0.0000 chunk 140 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 455 optimal weight: 40.0000 chunk 488 optimal weight: 9.9990 chunk 354 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 563 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1687 HIS A2401 HIS ** B 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 966 HIS ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1729 GLN B2072 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN E 547 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 908 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 58164 Z= 0.151 Angle : 0.571 14.437 78943 Z= 0.283 Chirality : 0.040 0.345 9158 Planarity : 0.003 0.048 10144 Dihedral : 3.851 23.549 8001 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 3.02 % Allowed : 21.48 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.10), residues: 7360 helix: 1.55 (0.08), residues: 4661 sheet: -0.15 (0.28), residues: 342 loop : -1.67 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 297 HIS 0.013 0.001 HIS B 966 PHE 0.034 0.001 PHE A 705 TYR 0.018 0.001 TYR B1232 ARG 0.006 0.000 ARG B1238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 710 time to evaluate : 4.871 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: A 807 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: A 940 ASN cc_start: 0.8565 (t0) cc_final: 0.8358 (t0) REVERT: A 1107 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8360 (pp) REVERT: A 1141 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8070 (ttm-80) REVERT: A 1203 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7584 (ptp90) REVERT: A 1225 GLU cc_start: 0.5789 (mp0) cc_final: 0.5582 (mp0) REVERT: A 1282 GLU cc_start: 0.8779 (tt0) cc_final: 0.8200 (mm-30) REVERT: A 1458 ASP cc_start: 0.8041 (m-30) cc_final: 0.7260 (t0) REVERT: A 1487 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 1523 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7525 (mt) REVERT: A 1649 ASP cc_start: 0.8208 (t0) cc_final: 0.7057 (p0) REVERT: A 1719 HIS cc_start: 0.8533 (t70) cc_final: 0.8234 (t-170) REVERT: A 1921 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8616 (mp0) REVERT: A 1988 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6850 (p-80) REVERT: A 2011 MET cc_start: 0.8541 (tmm) cc_final: 0.8270 (tmm) REVERT: A 2338 ASP cc_start: 0.8141 (t70) cc_final: 0.7517 (t0) REVERT: A 2382 MET cc_start: 0.8558 (tpp) cc_final: 0.8313 (tpp) REVERT: A 2409 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 2424 ASP cc_start: 0.8380 (t0) cc_final: 0.7975 (t0) REVERT: B 621 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7225 (tp30) REVERT: B 658 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9138 (mttt) REVERT: B 825 MET cc_start: 0.8586 (ttp) cc_final: 0.8330 (mmm) REVERT: B 1385 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: B 1422 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7935 (ttpp) REVERT: B 1458 ASP cc_start: 0.8295 (m-30) cc_final: 0.7633 (t0) REVERT: B 1487 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8568 (mm) REVERT: B 1523 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7545 (mt) REVERT: B 1687 HIS cc_start: 0.7829 (m90) cc_final: 0.7628 (m170) REVERT: B 1719 HIS cc_start: 0.8307 (t70) cc_final: 0.7807 (t-170) REVERT: B 1921 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8689 (mt-10) REVERT: B 1988 HIS cc_start: 0.7700 (p-80) cc_final: 0.6950 (p-80) REVERT: B 2155 SER cc_start: 0.8806 (t) cc_final: 0.8589 (p) REVERT: B 2327 MET cc_start: 0.9173 (tpt) cc_final: 0.8899 (tpt) REVERT: B 2329 MET cc_start: 0.8428 (tpp) cc_final: 0.8199 (tpp) REVERT: B 2338 ASP cc_start: 0.8191 (t0) cc_final: 0.7697 (t70) REVERT: B 2415 MET cc_start: 0.7668 (tpp) cc_final: 0.7443 (ttt) REVERT: C 101 TYR cc_start: 0.6930 (p90) cc_final: 0.6692 (p90) REVERT: C 142 GLU cc_start: 0.7253 (mm-30) cc_final: 0.5702 (mp0) REVERT: C 147 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7716 (t70) REVERT: D 101 TYR cc_start: 0.6939 (p90) cc_final: 0.6630 (p90) REVERT: D 170 GLU cc_start: 0.7997 (mp0) cc_final: 0.7777 (mp0) REVERT: D 247 TRP cc_start: 0.6194 (OUTLIER) cc_final: 0.5900 (m100) REVERT: E 76 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7411 (ptmm) REVERT: E 175 ASP cc_start: 0.8340 (t0) cc_final: 0.7559 (t0) REVERT: E 198 ASN cc_start: 0.9364 (t0) cc_final: 0.8964 (t0) REVERT: E 254 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7803 (pp) REVERT: E 382 ARG cc_start: 0.8177 (mmt90) cc_final: 0.7942 (mmt90) REVERT: E 397 SER cc_start: 0.9354 (t) cc_final: 0.8824 (p) REVERT: E 675 MET cc_start: 0.8440 (tpp) cc_final: 0.8234 (tpp) REVERT: E 749 ASN cc_start: 0.8138 (m-40) cc_final: 0.7749 (m-40) REVERT: E 772 ASP cc_start: 0.9017 (t70) cc_final: 0.8724 (t0) REVERT: E 958 GLN cc_start: 0.7438 (mm110) cc_final: 0.6968 (mt0) REVERT: E 968 CYS cc_start: 0.9201 (m) cc_final: 0.8750 (m) REVERT: E 998 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7896 (tppt) REVERT: E 1432 ASP cc_start: 0.8430 (t0) cc_final: 0.8032 (t0) REVERT: E 1607 MET cc_start: 0.5658 (mmp) cc_final: 0.5295 (mmm) REVERT: F 175 ASP cc_start: 0.8233 (t0) cc_final: 0.7484 (t0) REVERT: F 198 ASN cc_start: 0.9384 (t0) cc_final: 0.9051 (t0) REVERT: F 254 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7924 (pp) REVERT: F 360 ASP cc_start: 0.8296 (p0) cc_final: 0.8048 (m-30) REVERT: F 397 SER cc_start: 0.9350 (t) cc_final: 0.8821 (p) REVERT: F 520 ILE cc_start: 0.4059 (OUTLIER) cc_final: 0.3202 (tp) REVERT: F 544 LEU cc_start: 0.8563 (mp) cc_final: 0.8310 (mm) REVERT: F 749 ASN cc_start: 0.8216 (m-40) cc_final: 0.8003 (m-40) REVERT: F 968 CYS cc_start: 0.9043 (m) cc_final: 0.8617 (m) REVERT: F 972 LEU cc_start: 0.8751 (tp) cc_final: 0.8521 (tp) REVERT: F 998 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8574 (mtmt) REVERT: F 1432 ASP cc_start: 0.8687 (t0) cc_final: 0.8197 (t0) REVERT: F 1484 ARG cc_start: 0.6537 (ptt180) cc_final: 0.5531 (tpp-160) REVERT: G 108 TRP cc_start: 0.6917 (t-100) cc_final: 0.5726 (t-100) REVERT: H 108 TRP cc_start: 0.6430 (t-100) cc_final: 0.5526 (t-100) outliers start: 174 outliers final: 128 residues processed: 841 average time/residue: 0.5048 time to fit residues: 737.9334 Evaluate side-chains 797 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 653 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1082 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1141 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1902 ASP Chi-restraints excluded: chain A residue 1903 THR Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 1930 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2005 LEU Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1031 MET Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1122 PHE Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1347 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1422 LYS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1523 LEU Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1805 LYS Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2151 ILE Chi-restraints excluded: chain B residue 2222 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2419 GLU Chi-restraints excluded: chain B residue 2541 CYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 TRP Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1427 LEU Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 460 ASP Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 591 LEU Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1427 LEU Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 652 optimal weight: 0.6980 chunk 686 optimal weight: 2.9990 chunk 626 optimal weight: 5.9990 chunk 668 optimal weight: 6.9990 chunk 402 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 524 optimal weight: 0.9980 chunk 205 optimal weight: 0.0370 chunk 603 optimal weight: 5.9990 chunk 632 optimal weight: 0.9990 chunk 665 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 GLN A1183 GLN A1348 GLN A1687 HIS A1959 GLN ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 447 HIS E 547 ASN E 908 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 908 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 58164 Z= 0.148 Angle : 0.580 18.242 78943 Z= 0.284 Chirality : 0.040 0.352 9158 Planarity : 0.003 0.056 10144 Dihedral : 3.803 22.911 8001 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.14 % Favored : 95.72 % Rotamer: Outliers : 2.71 % Allowed : 22.18 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.10), residues: 7360 helix: 1.58 (0.08), residues: 4679 sheet: -0.11 (0.28), residues: 340 loop : -1.66 (0.13), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 297 HIS 0.009 0.000 HIS A 759 PHE 0.049 0.001 PHE B 705 TYR 0.025 0.001 TYR A2088 ARG 0.012 0.000 ARG A2430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 703 time to evaluate : 4.907 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: A 807 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 1107 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8437 (pp) REVERT: A 1141 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: A 1203 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7546 (ptp90) REVERT: A 1282 GLU cc_start: 0.8775 (tt0) cc_final: 0.8220 (mm-30) REVERT: A 1440 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: A 1458 ASP cc_start: 0.8032 (m-30) cc_final: 0.7164 (t0) REVERT: A 1487 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 1523 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 1649 ASP cc_start: 0.8230 (t0) cc_final: 0.7127 (p0) REVERT: A 1921 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: A 1988 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6798 (p-80) REVERT: A 2011 MET cc_start: 0.8561 (tmm) cc_final: 0.8303 (tmm) REVERT: A 2338 ASP cc_start: 0.8218 (t70) cc_final: 0.7623 (t0) REVERT: A 2382 MET cc_start: 0.8530 (tpp) cc_final: 0.8292 (tpp) REVERT: B 621 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7216 (tp30) REVERT: B 658 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9065 (mmmt) REVERT: B 825 MET cc_start: 0.8552 (ttp) cc_final: 0.8346 (mmm) REVERT: B 1385 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8352 (tp30) REVERT: B 1458 ASP cc_start: 0.8323 (m-30) cc_final: 0.7644 (t0) REVERT: B 1487 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8507 (mm) REVERT: B 1523 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7562 (mt) REVERT: B 1578 MET cc_start: 0.8039 (tpt) cc_final: 0.7836 (tpp) REVERT: B 1719 HIS cc_start: 0.8315 (t70) cc_final: 0.7801 (t-170) REVERT: B 1921 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8669 (mt-10) REVERT: B 1988 HIS cc_start: 0.7705 (p-80) cc_final: 0.6969 (p-80) REVERT: B 2033 GLU cc_start: 0.8269 (tp30) cc_final: 0.7887 (tp30) REVERT: B 2036 ARG cc_start: 0.8798 (tmm160) cc_final: 0.8584 (tmm160) REVERT: B 2155 SER cc_start: 0.8814 (t) cc_final: 0.8576 (p) REVERT: B 2315 ASP cc_start: 0.7976 (m-30) cc_final: 0.7707 (m-30) REVERT: B 2327 MET cc_start: 0.9056 (tpt) cc_final: 0.8774 (tpt) REVERT: B 2338 ASP cc_start: 0.8252 (t0) cc_final: 0.7602 (t70) REVERT: B 2415 MET cc_start: 0.7551 (tpp) cc_final: 0.7316 (ttt) REVERT: C 101 TYR cc_start: 0.6919 (p90) cc_final: 0.6676 (p90) REVERT: C 142 GLU cc_start: 0.7311 (mm-30) cc_final: 0.5844 (mp0) REVERT: D 101 TYR cc_start: 0.6989 (p90) cc_final: 0.6666 (p90) REVERT: D 170 GLU cc_start: 0.7984 (mp0) cc_final: 0.7757 (mp0) REVERT: D 247 TRP cc_start: 0.6193 (OUTLIER) cc_final: 0.5929 (m100) REVERT: E 175 ASP cc_start: 0.8334 (t0) cc_final: 0.7549 (t0) REVERT: E 198 ASN cc_start: 0.9345 (t0) cc_final: 0.8991 (t0) REVERT: E 254 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7811 (pp) REVERT: E 397 SER cc_start: 0.9351 (t) cc_final: 0.8813 (p) REVERT: E 749 ASN cc_start: 0.8128 (m-40) cc_final: 0.7739 (m-40) REVERT: E 772 ASP cc_start: 0.9015 (t70) cc_final: 0.8730 (t0) REVERT: E 958 GLN cc_start: 0.7480 (mm110) cc_final: 0.7050 (mt0) REVERT: E 968 CYS cc_start: 0.9183 (m) cc_final: 0.8744 (m) REVERT: E 1432 ASP cc_start: 0.8504 (t0) cc_final: 0.8222 (t0) REVERT: E 1607 MET cc_start: 0.5619 (mmp) cc_final: 0.5262 (mmm) REVERT: F 111 ILE cc_start: 0.8829 (mm) cc_final: 0.8508 (tp) REVERT: F 175 ASP cc_start: 0.8187 (t0) cc_final: 0.7475 (t0) REVERT: F 198 ASN cc_start: 0.9386 (t0) cc_final: 0.9085 (t0) REVERT: F 360 ASP cc_start: 0.8297 (p0) cc_final: 0.8021 (m-30) REVERT: F 397 SER cc_start: 0.9342 (t) cc_final: 0.8816 (p) REVERT: F 520 ILE cc_start: 0.4053 (OUTLIER) cc_final: 0.3206 (tp) REVERT: F 544 LEU cc_start: 0.8556 (mp) cc_final: 0.8297 (mm) REVERT: F 749 ASN cc_start: 0.8208 (m-40) cc_final: 0.7994 (m-40) REVERT: F 772 ASP cc_start: 0.9190 (t70) cc_final: 0.8965 (t0) REVERT: F 968 CYS cc_start: 0.9048 (m) cc_final: 0.8621 (m) REVERT: F 972 LEU cc_start: 0.8738 (tp) cc_final: 0.8506 (tp) REVERT: F 998 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8565 (mtmt) REVERT: F 1432 ASP cc_start: 0.8675 (t0) cc_final: 0.8189 (t0) REVERT: F 1484 ARG cc_start: 0.6527 (ptt180) cc_final: 0.5551 (tpp-160) REVERT: F 1671 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7688 (ttp80) REVERT: H 108 TRP cc_start: 0.6429 (t-100) cc_final: 0.5547 (t-100) outliers start: 156 outliers final: 124 residues processed: 818 average time/residue: 0.5143 time to fit residues: 731.7108 Evaluate side-chains 794 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 656 time to evaluate : 4.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1082 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1141 ARG Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1902 ASP Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 1930 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2005 LEU Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2428 ASN Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1122 PHE Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1347 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1523 LEU Chi-restraints excluded: chain B residue 1590 MET Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1805 LYS Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2222 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2419 GLU Chi-restraints excluded: chain B residue 2541 CYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 TRP Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 347 ILE Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1427 LEU Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 440 HIS Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1427 LEU Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 438 optimal weight: 7.9990 chunk 706 optimal weight: 0.2980 chunk 431 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 491 optimal weight: 4.9990 chunk 741 optimal weight: 30.0000 chunk 682 optimal weight: 0.9980 chunk 590 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 455 optimal weight: 0.7980 chunk 361 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1026 HIS A1687 HIS A2385 ASN B 966 HIS ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 HIS E 547 ASN E 908 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 908 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 58164 Z= 0.150 Angle : 0.588 17.072 78943 Z= 0.287 Chirality : 0.040 0.337 9158 Planarity : 0.003 0.047 10144 Dihedral : 3.757 23.280 8001 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.17 % Favored : 95.69 % Rotamer: Outliers : 2.62 % Allowed : 22.54 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.10), residues: 7360 helix: 1.62 (0.08), residues: 4669 sheet: -0.07 (0.28), residues: 340 loop : -1.58 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 297 HIS 0.008 0.001 HIS B 966 PHE 0.047 0.001 PHE B 705 TYR 0.020 0.001 TYR A2088 ARG 0.008 0.000 ARG B1238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14720 Ramachandran restraints generated. 7360 Oldfield, 0 Emsley, 7360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 689 time to evaluate : 5.018 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: A 759 HIS cc_start: 0.7875 (m170) cc_final: 0.7450 (m170) REVERT: A 807 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: A 1107 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8453 (pp) REVERT: A 1141 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8107 (ttm-80) REVERT: A 1203 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.7610 (ptp90) REVERT: A 1282 GLU cc_start: 0.8770 (tt0) cc_final: 0.8237 (mm-30) REVERT: A 1440 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8073 (m-10) REVERT: A 1458 ASP cc_start: 0.8026 (m-30) cc_final: 0.7149 (t0) REVERT: A 1523 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7544 (mt) REVERT: A 1649 ASP cc_start: 0.8276 (t0) cc_final: 0.7137 (p0) REVERT: A 1719 HIS cc_start: 0.8516 (t70) cc_final: 0.8186 (t-170) REVERT: A 1921 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: A 1988 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6781 (p-80) REVERT: A 2011 MET cc_start: 0.8574 (tmm) cc_final: 0.8339 (tmm) REVERT: A 2338 ASP cc_start: 0.8233 (t70) cc_final: 0.7643 (t0) REVERT: A 2382 MET cc_start: 0.8551 (tpp) cc_final: 0.8302 (tpp) REVERT: A 2431 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8368 (pp) REVERT: B 621 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7215 (tp30) REVERT: B 658 LYS cc_start: 0.9384 (mmmm) cc_final: 0.9060 (mmmt) REVERT: B 863 THR cc_start: 0.9126 (p) cc_final: 0.8745 (t) REVERT: B 1364 MET cc_start: 0.8702 (mmm) cc_final: 0.8448 (mmm) REVERT: B 1385 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8356 (tp30) REVERT: B 1458 ASP cc_start: 0.8277 (m-30) cc_final: 0.7617 (t0) REVERT: B 1487 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 1523 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7541 (mt) REVERT: B 1578 MET cc_start: 0.8056 (tpt) cc_final: 0.7825 (tpp) REVERT: B 1719 HIS cc_start: 0.8344 (t70) cc_final: 0.7841 (t-170) REVERT: B 1921 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8669 (mt-10) REVERT: B 1988 HIS cc_start: 0.7703 (p-80) cc_final: 0.6951 (p-80) REVERT: B 2033 GLU cc_start: 0.8294 (tp30) cc_final: 0.7886 (tp30) REVERT: B 2036 ARG cc_start: 0.8879 (tmm160) cc_final: 0.8647 (tmm160) REVERT: B 2155 SER cc_start: 0.8713 (t) cc_final: 0.8495 (p) REVERT: B 2175 MET cc_start: 0.8600 (tpp) cc_final: 0.8168 (tpp) REVERT: B 2315 ASP cc_start: 0.7981 (m-30) cc_final: 0.7710 (m-30) REVERT: B 2327 MET cc_start: 0.9068 (tpt) cc_final: 0.8765 (tpt) REVERT: B 2338 ASP cc_start: 0.8292 (t0) cc_final: 0.7651 (t70) REVERT: B 2415 MET cc_start: 0.7568 (tpp) cc_final: 0.7303 (ttt) REVERT: C 95 GLU cc_start: 0.8954 (tp30) cc_final: 0.8462 (tt0) REVERT: C 101 TYR cc_start: 0.6935 (p90) cc_final: 0.6711 (p90) REVERT: C 142 GLU cc_start: 0.7315 (mm-30) cc_final: 0.5839 (mp0) REVERT: D 101 TYR cc_start: 0.6975 (p90) cc_final: 0.6613 (p90) REVERT: D 170 GLU cc_start: 0.7958 (mp0) cc_final: 0.7730 (mp0) REVERT: D 247 TRP cc_start: 0.6196 (OUTLIER) cc_final: 0.5941 (m100) REVERT: E 76 LYS cc_start: 0.8102 (pttt) cc_final: 0.7661 (pttt) REVERT: E 175 ASP cc_start: 0.8345 (t0) cc_final: 0.7472 (t0) REVERT: E 198 ASN cc_start: 0.9346 (t0) cc_final: 0.9010 (t0) REVERT: E 254 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7778 (pp) REVERT: E 397 SER cc_start: 0.9353 (t) cc_final: 0.8812 (p) REVERT: E 508 ARG cc_start: 0.6179 (tpt170) cc_final: 0.5422 (mtm180) REVERT: E 702 VAL cc_start: 0.8773 (t) cc_final: 0.8542 (t) REVERT: E 749 ASN cc_start: 0.8124 (m-40) cc_final: 0.7735 (m-40) REVERT: E 772 ASP cc_start: 0.9041 (t70) cc_final: 0.8762 (t0) REVERT: E 791 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8023 (mttt) REVERT: E 958 GLN cc_start: 0.7458 (mm110) cc_final: 0.7027 (mt0) REVERT: E 968 CYS cc_start: 0.9199 (m) cc_final: 0.8766 (m) REVERT: E 998 LYS cc_start: 0.8256 (ttmt) cc_final: 0.8040 (tppt) REVERT: E 1432 ASP cc_start: 0.8499 (t0) cc_final: 0.8228 (t0) REVERT: E 1607 MET cc_start: 0.5710 (mmp) cc_final: 0.5365 (mmm) REVERT: F 111 ILE cc_start: 0.8820 (mm) cc_final: 0.8513 (tp) REVERT: F 175 ASP cc_start: 0.8228 (t0) cc_final: 0.7512 (t0) REVERT: F 198 ASN cc_start: 0.9332 (t0) cc_final: 0.9065 (t0) REVERT: F 360 ASP cc_start: 0.8302 (p0) cc_final: 0.8031 (m-30) REVERT: F 397 SER cc_start: 0.9350 (t) cc_final: 0.8820 (p) REVERT: F 520 ILE cc_start: 0.4128 (OUTLIER) cc_final: 0.3314 (tp) REVERT: F 544 LEU cc_start: 0.8561 (mp) cc_final: 0.8313 (mm) REVERT: F 675 MET cc_start: 0.8443 (tpp) cc_final: 0.8149 (tpt) REVERT: F 749 ASN cc_start: 0.8209 (m-40) cc_final: 0.7995 (m-40) REVERT: F 968 CYS cc_start: 0.9046 (m) cc_final: 0.8623 (m) REVERT: F 972 LEU cc_start: 0.8740 (tp) cc_final: 0.8504 (tp) REVERT: F 998 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8561 (mtmt) REVERT: F 1432 ASP cc_start: 0.8652 (t0) cc_final: 0.8198 (t0) REVERT: F 1484 ARG cc_start: 0.6467 (ptt180) cc_final: 0.5549 (tpp-160) REVERT: F 1671 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7659 (ttp80) REVERT: G 85 ASN cc_start: 0.7690 (t0) cc_final: 0.7319 (m-40) REVERT: H 108 TRP cc_start: 0.6446 (t-100) cc_final: 0.5544 (t-100) outliers start: 151 outliers final: 126 residues processed: 805 average time/residue: 0.5106 time to fit residues: 718.9494 Evaluate side-chains 797 residues out of total 6617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 656 time to evaluate : 4.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1082 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1141 ARG Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1440 PHE Chi-restraints excluded: chain A residue 1464 ASP Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1558 SER Chi-restraints excluded: chain A residue 1584 SER Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1902 ASP Chi-restraints excluded: chain A residue 1921 GLU Chi-restraints excluded: chain A residue 1930 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2005 LEU Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2276 ASP Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain A residue 2428 ASN Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2515 HIS Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 683 PHE Chi-restraints excluded: chain B residue 748 ARG Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 978 ILE Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 CYS Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1122 PHE Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain B residue 1194 MET Chi-restraints excluded: chain B residue 1347 SER Chi-restraints excluded: chain B residue 1385 GLU Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1487 LEU Chi-restraints excluded: chain B residue 1523 LEU Chi-restraints excluded: chain B residue 1590 MET Chi-restraints excluded: chain B residue 1686 ASP Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1902 ASP Chi-restraints excluded: chain B residue 1907 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2047 MET Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2222 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2353 ILE Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2419 GLU Chi-restraints excluded: chain B residue 2541 CYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 TRP Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 347 ILE Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 429 GLU Chi-restraints excluded: chain E residue 547 ASN Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 791 LYS Chi-restraints excluded: chain E residue 891 THR Chi-restraints excluded: chain E residue 895 LEU Chi-restraints excluded: chain E residue 926 SER Chi-restraints excluded: chain E residue 975 ILE Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1427 LEU Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 440 HIS Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain F residue 895 LEU Chi-restraints excluded: chain F residue 930 LEU Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1427 LEU Chi-restraints excluded: chain F residue 1675 GLU Chi-restraints excluded: chain F residue 1685 MET Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 468 optimal weight: 4.9990 chunk 628 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 544 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 591 optimal weight: 0.2980 chunk 247 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1687 HIS ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 ASN ** B1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 908 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.139297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099632 restraints weight = 123977.983| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.89 r_work: 0.3173 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.237 58164 Z= 0.193 Angle : 0.647 59.193 78943 Z= 0.338 Chirality : 0.041 1.047 9158 Planarity : 0.003 0.047 10144 Dihedral : 3.764 23.194 8001 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.23 % Favored : 95.64 % Rotamer: Outliers : 2.69 % Allowed : 22.56 % Favored : 74.75 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.10), residues: 7360 helix: 1.62 (0.08), residues: 4669 sheet: -0.07 (0.28), residues: 340 loop : -1.57 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 297 HIS 0.008 0.001 HIS A2189 PHE 0.043 0.001 PHE B 705 TYR 0.017 0.001 TYR A2088 ARG 0.006 0.000 ARG B1238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15082.26 seconds wall clock time: 263 minutes 54.89 seconds (15834.89 seconds total)