Starting phenix.real_space_refine on Sat Mar 16 05:38:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl9_41365/03_2024/8tl9_41365_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl9_41365/03_2024/8tl9_41365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl9_41365/03_2024/8tl9_41365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl9_41365/03_2024/8tl9_41365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl9_41365/03_2024/8tl9_41365_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl9_41365/03_2024/8tl9_41365_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 417 5.16 5 C 41495 2.51 5 N 11087 2.21 5 O 12045 1.98 5 H 65358 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 973": "OE1" <-> "OE2" Residue "A TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1000": "OE1" <-> "OE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1177": "OE1" <-> "OE2" Residue "A TYR 1272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1277": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A ASP 1331": "OD1" <-> "OD2" Residue "A ASP 1338": "OD1" <-> "OD2" Residue "A ASP 1358": "OD1" <-> "OD2" Residue "A ASP 1370": "OD1" <-> "OD2" Residue "A GLU 1384": "OE1" <-> "OE2" Residue "A ASP 1395": "OD1" <-> "OD2" Residue "A ASP 1404": "OD1" <-> "OD2" Residue "A GLU 1427": "OE1" <-> "OE2" Residue "A GLU 1430": "OE1" <-> "OE2" Residue "A ASP 1474": "OD1" <-> "OD2" Residue "A GLU 1603": "OE1" <-> "OE2" Residue "A GLU 1604": "OE1" <-> "OE2" Residue "A GLU 1630": "OE1" <-> "OE2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A GLU 1659": "OE1" <-> "OE2" Residue "A ASP 1681": "OD1" <-> "OD2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A GLU 1731": "OE1" <-> "OE2" Residue "A ASP 1739": "OD1" <-> "OD2" Residue "A GLU 1747": "OE1" <-> "OE2" Residue "A ASP 1762": "OD1" <-> "OD2" Residue "A ASP 1779": "OD1" <-> "OD2" Residue "A ASP 1887": "OD1" <-> "OD2" Residue "A TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1963": "OE1" <-> "OE2" Residue "A GLU 2011": "OE1" <-> "OE2" Residue "A GLU 2024": "OE1" <-> "OE2" Residue "A TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2125": "OE1" <-> "OE2" Residue "A GLU 2163": "OE1" <-> "OE2" Residue "A PHE 2177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2338": "OE1" <-> "OE2" Residue "A ASP 2449": "OD1" <-> "OD2" Residue "A ASP 2456": "OD1" <-> "OD2" Residue "A ASP 2497": "OD1" <-> "OD2" Residue "A GLU 2544": "OE1" <-> "OE2" Residue "A GLU 2557": "OE1" <-> "OE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 690": "OE1" <-> "OE2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 750": "OE1" <-> "OE2" Residue "B PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B PHE 875": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1046": "OE1" <-> "OE2" Residue "B ASP 1049": "OD1" <-> "OD2" Residue "B PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1208": "OD1" <-> "OD2" Residue "B GLU 1223": "OE1" <-> "OE2" Residue "B GLU 1262": "OE1" <-> "OE2" Residue "B GLU 1277": "OE1" <-> "OE2" Residue "B ASP 1301": "OD1" <-> "OD2" Residue "B ASP 1331": "OD1" <-> "OD2" Residue "B ASP 1370": "OD1" <-> "OD2" Residue "B PHE 1416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1603": "OE1" <-> "OE2" Residue "B GLU 1633": "OE1" <-> "OE2" Residue "B TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2009": "OD1" <-> "OD2" Residue "B ASP 2112": "OD1" <-> "OD2" Residue "B GLU 2125": "OE1" <-> "OE2" Residue "B GLU 2134": "OE1" <-> "OE2" Residue "B GLU 2163": "OE1" <-> "OE2" Residue "B PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2400": "OD1" <-> "OD2" Residue "B GLU 2532": "OE1" <-> "OE2" Residue "B GLU 2544": "OE1" <-> "OE2" Residue "B ASP 2600": "OD1" <-> "OD2" Residue "B PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C ASP 593": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 614": "OE1" <-> "OE2" Residue "C GLU 616": "OE1" <-> "OE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C GLU 750": "OE1" <-> "OE2" Residue "C PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 787": "OD1" <-> "OD2" Residue "C ASP 824": "OD1" <-> "OD2" Residue "C GLU 1000": "OE1" <-> "OE2" Residue "C ASP 1026": "OD1" <-> "OD2" Residue "C GLU 1046": "OE1" <-> "OE2" Residue "C PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1105": "OE1" <-> "OE2" Residue "C TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1125": "OE1" <-> "OE2" Residue "C GLU 1310": "OE1" <-> "OE2" Residue "C PHE 1416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1604": "OE1" <-> "OE2" Residue "C GLU 1639": "OE1" <-> "OE2" Residue "C GLU 1656": "OE1" <-> "OE2" Residue "C ASP 1791": "OD1" <-> "OD2" Residue "C ASP 1887": "OD1" <-> "OD2" Residue "C TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1968": "OD1" <-> "OD2" Residue "C ASP 2027": "OD1" <-> "OD2" Residue "C ASP 2112": "OD1" <-> "OD2" Residue "C GLU 2150": "OE1" <-> "OE2" Residue "C ASP 2173": "OD1" <-> "OD2" Residue "C PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 2347": "OD1" <-> "OD2" Residue "C TYR 2350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 2393": "OD1" <-> "OD2" Residue "C ASP 2456": "OD1" <-> "OD2" Residue "C ASP 2486": "OD1" <-> "OD2" Residue "C PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 2522": "OD1" <-> "OD2" Residue "C GLU 2526": "OE1" <-> "OE2" Residue "C GLU 2557": "OE1" <-> "OE2" Residue "C TYR 2589": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 572": "OE1" <-> "OE2" Residue "D ASP 593": "OD1" <-> "OD2" Residue "D TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 767": "OE1" <-> "OE2" Residue "D GLU 805": "OE1" <-> "OE2" Residue "D TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 847": "OE1" <-> "OE2" Residue "D GLU 862": "OE1" <-> "OE2" Residue "D ASP 961": "OD1" <-> "OD2" Residue "D ASP 1006": "OD1" <-> "OD2" Residue "D PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1049": "OD1" <-> "OD2" Residue "D GLU 1050": "OE1" <-> "OE2" Residue "D GLU 1177": "OE1" <-> "OE2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D GLU 1277": "OE1" <-> "OE2" Residue "D ASP 1301": "OD1" <-> "OD2" Residue "D GLU 1310": "OE1" <-> "OE2" Residue "D TYR 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1370": "OD1" <-> "OD2" Residue "D TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1430": "OE1" <-> "OE2" Residue "D GLU 1442": "OE1" <-> "OE2" Residue "D GLU 1456": "OE1" <-> "OE2" Residue "D ASP 1474": "OD1" <-> "OD2" Residue "D ASP 1587": "OD1" <-> "OD2" Residue "D GLU 1593": "OE1" <-> "OE2" Residue "D GLU 1633": "OE1" <-> "OE2" Residue "D GLU 1639": "OE1" <-> "OE2" Residue "D ASP 1681": "OD1" <-> "OD2" Residue "D TYR 1694": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1739": "OD1" <-> "OD2" Residue "D GLU 1752": "OE1" <-> "OE2" Residue "D GLU 1963": "OE1" <-> "OE2" Residue "D ASP 2009": "OD1" <-> "OD2" Residue "D GLU 2024": "OE1" <-> "OE2" Residue "D GLU 2118": "OE1" <-> "OE2" Residue "D ASP 2130": "OD1" <-> "OD2" Residue "D PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 2225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2352": "OE1" <-> "OE2" Residue "D ASP 2393": "OD1" <-> "OD2" Residue "D ASP 2456": "OD1" <-> "OD2" Residue "D PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2539": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2562": "OE1" <-> "OE2" Residue "D ASP 2582": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 130434 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 32350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1989, 32350 Classifications: {'peptide': 1989} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1933} Chain breaks: 13 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 32312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1987, 32312 Classifications: {'peptide': 1987} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1931} Chain breaks: 13 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 32587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2005, 32587 Classifications: {'peptide': 2005} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1949} Chain breaks: 12 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 32957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 32957 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 2, 'PTRANS': 56, 'TRANS': 1975} Chain breaks: 11 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31094 SG CYS A2538 137.318 134.464 93.803 1.00 79.87 S ATOM 31143 SG CYS A2541 135.221 136.427 91.299 1.00 62.30 S ATOM 63406 SG CYS B2538 113.523 150.552 93.849 1.00 88.10 S ATOM 63455 SG CYS B2541 111.925 148.057 91.437 1.00 62.84 S ATOM 95993 SG CYS C2538 97.831 126.064 93.602 1.00 82.70 S ATOM 96042 SG CYS C2541 100.326 124.853 90.999 1.00 73.98 S ATOM A0MC6 SG CYS D2538 121.708 110.546 93.953 1.00 85.96 S ATOM A0MDJ SG CYS D2541 123.181 112.983 91.380 1.00 65.26 S Time building chain proxies: 41.80, per 1000 atoms: 0.32 Number of scatterers: 130434 At special positions: 0 Unit cell: (237.888, 251.104, 178.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 417 16.00 P 24 15.00 O 12045 8.00 N 11087 7.00 C 41495 6.00 H 65358 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.04 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.04 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 82.17 Conformation dependent library (CDL) restraints added in 9.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2541 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2538 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B3001 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2541 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2538 " pdb=" ZN C3001 " pdb="ZN ZN C3001 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C3001 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2541 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2538 " pdb=" ZN D3001 " pdb="ZN ZN D3001 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D3001 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2541 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2538 " Number of angles added : 4 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15392 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 407 helices and 31 sheets defined 76.7% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 55.28 Creating SS restraints... Processing helix chain 'A' and resid 278 through 283 removed outlier: 5.614A pdb=" N TRP A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 4.317A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N PHE A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 367' Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.659A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 514 through 527 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 537 through 544 removed outlier: 4.176A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 565 removed outlier: 5.101A pdb=" N TYR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 removed outlier: 3.573A pdb=" N LYS A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 590 through 603 removed outlier: 4.112A pdb=" N ARG A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.927A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 Processing helix chain 'A' and resid 659 through 666 removed outlier: 5.218A pdb=" N ASP A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 659 through 666' Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 719 through 741 Processing helix chain 'A' and resid 745 through 756 removed outlier: 4.818A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 811 through 820 removed outlier: 3.586A pdb=" N ASP A 816 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 831 removed outlier: 3.681A pdb=" N ASN A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS A 829 " --> pdb=" O ASP A 825 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 848 removed outlier: 5.326A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 874 removed outlier: 3.540A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 3.890A pdb=" N ARG A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 1002 removed outlier: 3.517A pdb=" N MET A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1037 removed outlier: 3.567A pdb=" N ALA A1034 " --> pdb=" O GLU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1066 removed outlier: 3.647A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.856A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 Processing helix chain 'A' and resid 1100 through 1128 removed outlier: 5.439A pdb=" N GLU A1125 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 3.684A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 Processing helix chain 'A' and resid 1202 through 1212 Processing helix chain 'A' and resid 1218 through 1237 Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 3.554A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 Processing helix chain 'A' and resid 1271 through 1278 Processing helix chain 'A' and resid 1279 through 1293 Processing helix chain 'A' and resid 1297 through 1309 removed outlier: 3.520A pdb=" N LEU A1303 " --> pdb=" O TYR A1299 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 Processing helix chain 'A' and resid 1338 through 1353 Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 5.576A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.772A pdb=" N LYS A1386 " --> pdb=" O TYR A1382 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1393 through 1402 Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1428 through 1458 removed outlier: 3.611A pdb=" N TYR A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN A1435 " --> pdb=" O ILE A1431 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N HIS A1436 " --> pdb=" O TYR A1432 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TRP A1438 " --> pdb=" O SER A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.676A pdb=" N VAL A1471 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1489 removed outlier: 3.661A pdb=" N ASN A1487 " --> pdb=" O PRO A1483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR A1489 " --> pdb=" O SER A1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1483 through 1489' Processing helix chain 'A' and resid 1490 through 1495 Processing helix chain 'A' and resid 1496 through 1512 Proline residue: A1512 - end of helix Processing helix chain 'A' and resid 1516 through 1534 Processing helix chain 'A' and resid 1541 through 1557 Processing helix chain 'A' and resid 1587 through 1624 Proline residue: A1608 - end of helix removed outlier: 3.525A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A1617 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A1619 " --> pdb=" O SER A1615 " (cutoff:3.500A) Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 removed outlier: 3.753A pdb=" N GLY A1641 " --> pdb=" O ARG A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1655 Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 5.261A pdb=" N LYS A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1695 Processing helix chain 'A' and resid 1718 through 1732 Processing helix chain 'A' and resid 1733 through 1744 Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1765 through 1779 Processing helix chain 'A' and resid 1781 through 1807 Processing helix chain 'A' and resid 1864 through 1882 removed outlier: 3.662A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1895 removed outlier: 3.605A pdb=" N ARG A1893 " --> pdb=" O GLN A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1916 Processing helix chain 'A' and resid 1917 through 1923 Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 5.059A pdb=" N ASN A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1931 through 1949 removed outlier: 4.722A pdb=" N GLY A1935 " --> pdb=" O GLU A1931 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU A1936 " --> pdb=" O ASP A1932 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1962 Processing helix chain 'A' and resid 1965 through 1976 removed outlier: 3.932A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A1974 " --> pdb=" O ILE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1985 removed outlier: 4.146A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 Processing helix chain 'A' and resid 2010 through 2021 removed outlier: 3.722A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2036 removed outlier: 3.653A pdb=" N TYR A2033 " --> pdb=" O ILE A2029 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A2034 " --> pdb=" O LYS A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2062 Processing helix chain 'A' and resid 2064 through 2073 Proline residue: A2073 - end of helix Processing helix chain 'A' and resid 2112 through 2121 Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 4.353A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU A2147 " --> pdb=" O ILE A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2141 through 2147' Processing helix chain 'A' and resid 2148 through 2158 Processing helix chain 'A' and resid 2167 through 2192 removed outlier: 4.492A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) Proline residue: A2192 - end of helix Processing helix chain 'A' and resid 2193 through 2201 removed outlier: 3.674A pdb=" N PHE A2197 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2222 Processing helix chain 'A' and resid 2261 through 2276 Processing helix chain 'A' and resid 2277 through 2310 removed outlier: 6.317A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A2310 " --> pdb=" O THR A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2318 removed outlier: 5.841A pdb=" N MET A2318 " --> pdb=" O MET A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2319 through 2336 Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 4.749A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A2353 " --> pdb=" O ILE A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2364 removed outlier: 3.540A pdb=" N SER A2361 " --> pdb=" O ASN A2357 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2390 removed outlier: 3.567A pdb=" N ILE A2369 " --> pdb=" O ASN A2365 " (cutoff:3.500A) Processing helix chain 'A' and resid 2457 through 2472 removed outlier: 3.979A pdb=" N LEU A2470 " --> pdb=" O MET A2466 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A2471 " --> pdb=" O ASN A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.211A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2537 removed outlier: 3.842A pdb=" N ILE A2512 " --> pdb=" O VAL A2508 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2550 removed outlier: 4.165A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A2549 " --> pdb=" O ARG A2545 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN A2550 " --> pdb=" O ASP A2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2544 through 2550' Processing helix chain 'A' and resid 2554 through 2561 Processing helix chain 'A' and resid 2564 through 2578 Processing helix chain 'A' and resid 2584 through 2597 Processing helix chain 'A' and resid 2607 through 2612 Processing helix chain 'A' and resid 2598 through 2603 removed outlier: 4.629A pdb=" N TRP A2601 " --> pdb=" O ASN A2598 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A2602 " --> pdb=" O LEU A2599 " (cutoff:3.500A) Proline residue: A2603 - end of helix No H-bonds generated for 'chain 'A' and resid 2598 through 2603' Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.891A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 277' Processing helix chain 'B' and resid 278 through 283 removed outlier: 5.415A pdb=" N TRP B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 4.366A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 367' Processing helix chain 'B' and resid 435 through 462 removed outlier: 3.797A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 514 through 527 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 537 through 544 removed outlier: 4.487A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP B 543 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLN B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 565 Processing helix chain 'B' and resid 567 through 578 removed outlier: 3.818A pdb=" N LYS B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 585 Processing helix chain 'B' and resid 590 through 603 removed outlier: 4.023A pdb=" N ARG B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'B' and resid 627 through 640 removed outlier: 4.138A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 658 Processing helix chain 'B' and resid 659 through 666 removed outlier: 4.742A pdb=" N ASP B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 659 through 666' Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 719 through 741 Processing helix chain 'B' and resid 744 through 756 removed outlier: 3.559A pdb=" N ILE B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 766 Processing helix chain 'B' and resid 770 through 785 Processing helix chain 'B' and resid 802 through 807 removed outlier: 3.549A pdb=" N ILE B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Proline residue: B 807 - end of helix No H-bonds generated for 'chain 'B' and resid 802 through 807' Processing helix chain 'B' and resid 811 through 821 removed outlier: 3.715A pdb=" N ASP B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 831 Processing helix chain 'B' and resid 832 through 848 removed outlier: 5.169A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 874 removed outlier: 3.538A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 removed outlier: 3.564A pdb=" N THR B 887 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 1002 Processing helix chain 'B' and resid 1024 through 1037 removed outlier: 3.574A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 5.206A pdb=" N ASP B1066 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.690A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 Processing helix chain 'B' and resid 1100 through 1128 removed outlier: 4.797A pdb=" N GLU B1125 " --> pdb=" O VAL B1121 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU B1126 " --> pdb=" O GLU B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.088A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1201 Processing helix chain 'B' and resid 1202 through 1212 Processing helix chain 'B' and resid 1218 through 1237 Processing helix chain 'B' and resid 1239 through 1250 Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1271 through 1278 Processing helix chain 'B' and resid 1279 through 1293 removed outlier: 3.586A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1309 removed outlier: 3.530A pdb=" N LYS B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 Processing helix chain 'B' and resid 1338 through 1354 removed outlier: 4.514A pdb=" N ASP B1354 " --> pdb=" O LYS B1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 5.313A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1392 removed outlier: 3.638A pdb=" N LYS B1386 " --> pdb=" O TYR B1382 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B1391 " --> pdb=" O CYS B1387 " (cutoff:3.500A) Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1402 Processing helix chain 'B' and resid 1406 through 1420 Processing helix chain 'B' and resid 1428 through 1458 removed outlier: 4.249A pdb=" N TYR B1432 " --> pdb=" O MET B1428 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASN B1435 " --> pdb=" O ILE B1431 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS B1436 " --> pdb=" O TYR B1432 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B1437 " --> pdb=" O THR B1433 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TRP B1438 " --> pdb=" O SER B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.961A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1483 through 1488 removed outlier: 3.676A pdb=" N ASN B1487 " --> pdb=" O PRO B1483 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1483 through 1488' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 4.140A pdb=" N THR B1493 " --> pdb=" O THR B1489 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1512 Proline residue: B1512 - end of helix Processing helix chain 'B' and resid 1515 through 1534 Processing helix chain 'B' and resid 1541 through 1557 Processing helix chain 'B' and resid 1587 through 1624 Proline residue: B1608 - end of helix removed outlier: 3.824A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B1616 " --> pdb=" O ALA B1612 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B1617 " --> pdb=" O GLU B1613 " (cutoff:3.500A) Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 Processing helix chain 'B' and resid 1642 through 1655 removed outlier: 3.690A pdb=" N LYS B1652 " --> pdb=" O ILE B1648 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B1653 " --> pdb=" O GLN B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.651A pdb=" N CYS B1662 " --> pdb=" O GLU B1658 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS B1675 " --> pdb=" O GLN B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1695 Processing helix chain 'B' and resid 1718 through 1732 Processing helix chain 'B' and resid 1733 through 1744 Processing helix chain 'B' and resid 1746 through 1762 Processing helix chain 'B' and resid 1765 through 1779 Processing helix chain 'B' and resid 1781 through 1807 Processing helix chain 'B' and resid 1864 through 1882 removed outlier: 3.833A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1885 through 1895 removed outlier: 3.507A pdb=" N ARG B1893 " --> pdb=" O GLN B1889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1902 through 1916 Processing helix chain 'B' and resid 1917 through 1923 Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 3.833A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1931 through 1949 removed outlier: 4.837A pdb=" N GLY B1935 " --> pdb=" O GLU B1931 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B1936 " --> pdb=" O ASP B1932 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1962 Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 4.161A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B1974 " --> pdb=" O ILE B1970 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B1975 " --> pdb=" O THR B1971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1985 removed outlier: 4.288A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 Processing helix chain 'B' and resid 2010 through 2021 removed outlier: 3.678A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2036 removed outlier: 3.789A pdb=" N TYR B2033 " --> pdb=" O ILE B2029 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B2034 " --> pdb=" O LYS B2030 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2062 removed outlier: 3.794A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2073 removed outlier: 3.541A pdb=" N GLN B2068 " --> pdb=" O ASN B2064 " (cutoff:3.500A) Proline residue: B2073 - end of helix Processing helix chain 'B' and resid 2112 through 2121 Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 4.383A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B2147 " --> pdb=" O ILE B2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2141 through 2147' Processing helix chain 'B' and resid 2148 through 2159 Processing helix chain 'B' and resid 2167 through 2192 removed outlier: 4.483A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) Proline residue: B2192 - end of helix Processing helix chain 'B' and resid 2193 through 2222 removed outlier: 4.035A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP B2204 " --> pdb=" O ARG B2200 " (cutoff:3.500A) Processing helix chain 'B' and resid 2261 through 2276 Processing helix chain 'B' and resid 2277 through 2310 removed outlier: 6.238A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B2310 " --> pdb=" O THR B2306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2318 removed outlier: 5.550A pdb=" N MET B2318 " --> pdb=" O MET B2314 " (cutoff:3.500A) Processing helix chain 'B' and resid 2319 through 2336 Processing helix chain 'B' and resid 2339 through 2353 removed outlier: 4.921A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU B2353 " --> pdb=" O ILE B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2364 removed outlier: 3.574A pdb=" N SER B2361 " --> pdb=" O ASN B2357 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2390 removed outlier: 3.502A pdb=" N ILE B2369 " --> pdb=" O ASN B2365 " (cutoff:3.500A) Processing helix chain 'B' and resid 2391 through 2396 removed outlier: 3.979A pdb=" N PHE B2395 " --> pdb=" O LEU B2391 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE B2396 " --> pdb=" O LYS B2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2391 through 2396' Processing helix chain 'B' and resid 2457 through 2472 removed outlier: 3.936A pdb=" N LEU B2470 " --> pdb=" O MET B2466 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B2471 " --> pdb=" O ASN B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.317A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2537 removed outlier: 3.882A pdb=" N ILE B2512 " --> pdb=" O VAL B2508 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.294A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B2549 " --> pdb=" O ARG B2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2544 through 2549' Processing helix chain 'B' and resid 2554 through 2561 Processing helix chain 'B' and resid 2564 through 2578 Processing helix chain 'B' and resid 2584 through 2597 Processing helix chain 'B' and resid 2607 through 2612 Processing helix chain 'B' and resid 2598 through 2603 removed outlier: 4.695A pdb=" N TRP B2601 " --> pdb=" O ASN B2598 " (cutoff:3.500A) Proline residue: B2603 - end of helix Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.684A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 277' Processing helix chain 'C' and resid 278 through 283 removed outlier: 5.709A pdb=" N TRP C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 removed outlier: 3.886A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 367' Processing helix chain 'C' and resid 435 through 461 removed outlier: 3.818A pdb=" N ILE C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'C' and resid 514 through 527 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 537 through 544 removed outlier: 4.430A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP C 543 " --> pdb=" O GLU C 539 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 565 removed outlier: 4.936A pdb=" N TYR C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 removed outlier: 3.920A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 585 Processing helix chain 'C' and resid 590 through 603 removed outlier: 3.781A pdb=" N ASN C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 627 through 640 removed outlier: 4.304A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 Processing helix chain 'C' and resid 658 through 666 removed outlier: 4.711A pdb=" N ASP C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 689 Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 719 through 741 Processing helix chain 'C' and resid 744 through 755 removed outlier: 4.419A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 766 Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 811 through 821 removed outlier: 3.989A pdb=" N ALA C 821 " --> pdb=" O SER C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 827 removed outlier: 3.833A pdb=" N LYS C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 848 removed outlier: 3.520A pdb=" N MET C 834 " --> pdb=" O PHE C 830 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 874 removed outlier: 3.712A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 removed outlier: 3.648A pdb=" N ARG C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR C 887 " --> pdb=" O ARG C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 1002 Processing helix chain 'C' and resid 1024 through 1037 removed outlier: 3.645A pdb=" N MET C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1066 removed outlier: 3.535A pdb=" N MET C1064 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.706A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1095 Processing helix chain 'C' and resid 1100 through 1128 removed outlier: 5.689A pdb=" N GLU C1125 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C1126 " --> pdb=" O GLU C1122 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP C1127 " --> pdb=" O LYS C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 3.949A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1201 Processing helix chain 'C' and resid 1202 through 1212 Processing helix chain 'C' and resid 1218 through 1237 removed outlier: 3.691A pdb=" N MET C1222 " --> pdb=" O ASP C1218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1251 removed outlier: 3.505A pdb=" N LYS C1248 " --> pdb=" O ALA C1244 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N HIS C1251 " --> pdb=" O HIS C1247 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 removed outlier: 3.554A pdb=" N GLU C1262 " --> pdb=" O LEU C1258 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C1263 " --> pdb=" O LEU C1259 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1278 Processing helix chain 'C' and resid 1279 through 1293 Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.660A pdb=" N LYS C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 Processing helix chain 'C' and resid 1338 through 1354 removed outlier: 4.383A pdb=" N ASP C1354 " --> pdb=" O LYS C1350 " (cutoff:3.500A) Processing helix chain 'C' and resid 1360 through 1378 removed outlier: 5.371A pdb=" N GLY C1378 " --> pdb=" O ALA C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1380 through 1391 Processing helix chain 'C' and resid 1392 through 1402 removed outlier: 3.766A pdb=" N VAL C1396 " --> pdb=" O PRO C1392 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS C1402 " --> pdb=" O SER C1398 " (cutoff:3.500A) Processing helix chain 'C' and resid 1406 through 1421 Processing helix chain 'C' and resid 1428 through 1434 removed outlier: 4.112A pdb=" N TYR C1432 " --> pdb=" O MET C1428 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1458 Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.585A pdb=" N VAL C1471 " --> pdb=" O TYR C1467 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 1489 through 1512 removed outlier: 4.947A pdb=" N THR C1493 " --> pdb=" O THR C1489 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR C1496 " --> pdb=" O GLN C1492 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE C1497 " --> pdb=" O THR C1493 " (cutoff:3.500A) Proline residue: C1512 - end of helix Processing helix chain 'C' and resid 1515 through 1537 removed outlier: 3.642A pdb=" N SER C1521 " --> pdb=" O GLN C1517 " (cutoff:3.500A) Processing helix chain 'C' and resid 1542 through 1557 Processing helix chain 'C' and resid 1587 through 1624 Proline residue: C1608 - end of helix removed outlier: 3.764A pdb=" N GLN C1611 " --> pdb=" O LYS C1607 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C1616 " --> pdb=" O ALA C1612 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C1617 " --> pdb=" O GLU C1613 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C1618 " --> pdb=" O LEU C1614 " (cutoff:3.500A) Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 removed outlier: 3.922A pdb=" N GLY C1641 " --> pdb=" O ARG C1637 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1655 Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 5.291A pdb=" N LYS C1675 " --> pdb=" O GLN C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1695 Processing helix chain 'C' and resid 1718 through 1732 Processing helix chain 'C' and resid 1733 through 1744 Processing helix chain 'C' and resid 1746 through 1762 Processing helix chain 'C' and resid 1765 through 1779 Processing helix chain 'C' and resid 1781 through 1807 Processing helix chain 'C' and resid 1864 through 1882 removed outlier: 3.944A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1885 through 1895 removed outlier: 3.703A pdb=" N ARG C1893 " --> pdb=" O GLN C1889 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C1895 " --> pdb=" O PHE C1891 " (cutoff:3.500A) Processing helix chain 'C' and resid 1902 through 1916 Processing helix chain 'C' and resid 1917 through 1923 Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 5.159A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1931 through 1949 removed outlier: 4.843A pdb=" N GLY C1935 " --> pdb=" O GLU C1931 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU C1936 " --> pdb=" O ASP C1932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1962 Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 4.090A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C1974 " --> pdb=" O ILE C1970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1985 removed outlier: 4.119A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 Processing helix chain 'C' and resid 2010 through 2021 removed outlier: 3.935A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2036 Processing helix chain 'C' and resid 2045 through 2062 removed outlier: 3.874A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) Processing helix chain 'C' and resid 2064 through 2072 removed outlier: 3.553A pdb=" N GLN C2068 " --> pdb=" O ASN C2064 " (cutoff:3.500A) Processing helix chain 'C' and resid 2112 through 2121 Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 4.319A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU C2147 " --> pdb=" O ILE C2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2141 through 2147' Processing helix chain 'C' and resid 2148 through 2159 Processing helix chain 'C' and resid 2167 through 2192 removed outlier: 4.571A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) Proline residue: C2192 - end of helix Processing helix chain 'C' and resid 2193 through 2223 removed outlier: 3.512A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP C2204 " --> pdb=" O ARG C2200 " (cutoff:3.500A) Processing helix chain 'C' and resid 2261 through 2276 Processing helix chain 'C' and resid 2277 through 2310 removed outlier: 6.241A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C2310 " --> pdb=" O THR C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2317 Processing helix chain 'C' and resid 2318 through 2336 Processing helix chain 'C' and resid 2340 through 2353 removed outlier: 4.671A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU C2353 " --> pdb=" O ILE C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2364 removed outlier: 4.057A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2390 removed outlier: 3.556A pdb=" N ILE C2369 " --> pdb=" O ASN C2365 " (cutoff:3.500A) Processing helix chain 'C' and resid 2391 through 2396 removed outlier: 3.944A pdb=" N PHE C2395 " --> pdb=" O LEU C2391 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE C2396 " --> pdb=" O LYS C2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2391 through 2396' Processing helix chain 'C' and resid 2457 through 2472 removed outlier: 4.038A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C2471 " --> pdb=" O ASN C2467 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.219A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2537 removed outlier: 3.954A pdb=" N ILE C2512 " --> pdb=" O VAL C2508 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.160A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2544 through 2549' Processing helix chain 'C' and resid 2554 through 2561 Processing helix chain 'C' and resid 2564 through 2578 Processing helix chain 'C' and resid 2584 through 2597 Processing helix chain 'C' and resid 2607 through 2612 Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.667A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 277' Processing helix chain 'D' and resid 362 through 367 removed outlier: 4.230A pdb=" N LEU D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE D 367 " --> pdb=" O ILE D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 362 through 367' Processing helix chain 'D' and resid 435 through 462 removed outlier: 3.841A pdb=" N ILE D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 514 through 527 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 537 through 544 removed outlier: 4.536A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP D 543 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 565 removed outlier: 4.886A pdb=" N TYR D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 removed outlier: 4.089A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 586 removed outlier: 5.273A pdb=" N GLY D 586 " --> pdb=" O GLN D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 603 removed outlier: 3.688A pdb=" N THR D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 610 Processing helix chain 'D' and resid 611 through 626 Processing helix chain 'D' and resid 627 through 640 removed outlier: 4.197A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 658 Processing helix chain 'D' and resid 659 through 666 removed outlier: 5.242A pdb=" N ASP D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 659 through 666' Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 719 through 741 Processing helix chain 'D' and resid 744 through 756 removed outlier: 4.204A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY D 756 " --> pdb=" O SER D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 766 Processing helix chain 'D' and resid 770 through 784 Processing helix chain 'D' and resid 811 through 821 removed outlier: 3.678A pdb=" N ASP D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA D 821 " --> pdb=" O SER D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 831 removed outlier: 4.223A pdb=" N LYS D 829 " --> pdb=" O ASP D 825 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 830 " --> pdb=" O LYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 848 removed outlier: 5.442A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 874 removed outlier: 3.704A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 removed outlier: 3.755A pdb=" N ARG D 886 " --> pdb=" O LEU D 882 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR D 887 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 1003 Proline residue: D1003 - end of helix Processing helix chain 'D' and resid 1024 through 1037 Processing helix chain 'D' and resid 1052 through 1066 removed outlier: 3.725A pdb=" N HIS D1065 " --> pdb=" O HIS D1061 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP D1066 " --> pdb=" O LEU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.828A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.693A pdb=" N GLN D1094 " --> pdb=" O HIS D1090 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D1095 " --> pdb=" O THR D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 3.623A pdb=" N SER D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU D1126 " --> pdb=" O GLU D1122 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1185 removed outlier: 4.102A pdb=" N GLN D1170 " --> pdb=" O SER D1166 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL D1185 " --> pdb=" O LYS D1181 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1201 removed outlier: 3.521A pdb=" N LYS D1192 " --> pdb=" O GLN D1188 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1212 Processing helix chain 'D' and resid 1218 through 1237 Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 4.182A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 Processing helix chain 'D' and resid 1271 through 1278 Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.757A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D1291 " --> pdb=" O VAL D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1297 through 1309 removed outlier: 4.257A pdb=" N LYS D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 4.218A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 Processing helix chain 'D' and resid 1360 through 1378 removed outlier: 3.718A pdb=" N TYR D1364 " --> pdb=" O SER D1360 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D1365 " --> pdb=" O PRO D1361 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY D1378 " --> pdb=" O ALA D1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1392 Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1393 through 1402 Processing helix chain 'D' and resid 1406 through 1420 removed outlier: 3.638A pdb=" N ALA D1412 " --> pdb=" O GLU D1408 " (cutoff:3.500A) Processing helix chain 'D' and resid 1428 through 1434 removed outlier: 4.099A pdb=" N TYR D1432 " --> pdb=" O MET D1428 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1458 removed outlier: 3.517A pdb=" N THR D1439 " --> pdb=" O ASN D1435 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.735A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) Processing helix chain 'D' and resid 1483 through 1489 removed outlier: 4.774A pdb=" N ASN D1487 " --> pdb=" O PRO D1483 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER D1488 " --> pdb=" O PHE D1484 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR D1489 " --> pdb=" O SER D1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1483 through 1489' Processing helix chain 'D' and resid 1490 through 1495 Processing helix chain 'D' and resid 1496 through 1511 Processing helix chain 'D' and resid 1516 through 1537 removed outlier: 3.960A pdb=" N SER D1521 " --> pdb=" O GLN D1517 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1570 removed outlier: 3.541A pdb=" N SER D1549 " --> pdb=" O ASP D1545 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D1550 " --> pdb=" O ALA D1546 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU D1552 " --> pdb=" O ILE D1548 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D1553 " --> pdb=" O SER D1549 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY D1555 " --> pdb=" O MET D1551 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA D1556 " --> pdb=" O LEU D1552 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D1557 " --> pdb=" O SER D1553 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER D1567 " --> pdb=" O GLN D1563 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER D1568 " --> pdb=" O ARG D1564 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D1569 " --> pdb=" O ASN D1565 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS D1570 " --> pdb=" O ALA D1566 " (cutoff:3.500A) Processing helix chain 'D' and resid 1571 through 1576 removed outlier: 4.312A pdb=" N ALA D1575 " --> pdb=" O ALA D1571 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE D1576 " --> pdb=" O THR D1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1571 through 1576' Processing helix chain 'D' and resid 1587 through 1624 removed outlier: 4.804A pdb=" N ILE D1591 " --> pdb=" O ASP D1587 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE D1592 " --> pdb=" O TYR D1588 " (cutoff:3.500A) Proline residue: D1608 - end of helix removed outlier: 3.532A pdb=" N VAL D1616 " --> pdb=" O ALA D1612 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D1617 " --> pdb=" O GLU D1613 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL D1618 " --> pdb=" O LEU D1614 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D1619 " --> pdb=" O SER D1615 " (cutoff:3.500A) Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 removed outlier: 3.688A pdb=" N SER D1640 " --> pdb=" O GLN D1636 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY D1641 " --> pdb=" O ARG D1637 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1655 removed outlier: 3.521A pdb=" N LYS D1652 " --> pdb=" O ILE D1648 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D1653 " --> pdb=" O GLN D1649 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 5.322A pdb=" N LYS D1675 " --> pdb=" O GLN D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1695 Processing helix chain 'D' and resid 1718 through 1732 Processing helix chain 'D' and resid 1733 through 1744 Processing helix chain 'D' and resid 1746 through 1762 Processing helix chain 'D' and resid 1765 through 1779 Processing helix chain 'D' and resid 1781 through 1807 Processing helix chain 'D' and resid 1864 through 1882 removed outlier: 3.898A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1895 removed outlier: 3.661A pdb=" N ARG D1893 " --> pdb=" O GLN D1889 " (cutoff:3.500A) Processing helix chain 'D' and resid 1902 through 1916 Processing helix chain 'D' and resid 1917 through 1923 Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 3.525A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1931 through 1949 removed outlier: 4.709A pdb=" N GLY D1935 " --> pdb=" O GLU D1931 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU D1936 " --> pdb=" O ASP D1932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1962 Processing helix chain 'D' and resid 1965 through 1976 removed outlier: 3.967A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1978 through 1985 removed outlier: 4.561A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 Processing helix chain 'D' and resid 2010 through 2021 removed outlier: 3.924A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2036 removed outlier: 3.578A pdb=" N TYR D2033 " --> pdb=" O ILE D2029 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2062 removed outlier: 3.931A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) Processing helix chain 'D' and resid 2064 through 2073 removed outlier: 3.613A pdb=" N GLN D2068 " --> pdb=" O ASN D2064 " (cutoff:3.500A) Proline residue: D2073 - end of helix Processing helix chain 'D' and resid 2112 through 2121 Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 4.379A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU D2147 " --> pdb=" O ILE D2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2141 through 2147' Processing helix chain 'D' and resid 2148 through 2158 Processing helix chain 'D' and resid 2167 through 2192 removed outlier: 4.483A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) Proline residue: D2192 - end of helix Processing helix chain 'D' and resid 2193 through 2201 removed outlier: 3.794A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) Processing helix chain 'D' and resid 2202 through 2222 Processing helix chain 'D' and resid 2261 through 2276 Processing helix chain 'D' and resid 2277 through 2310 removed outlier: 6.439A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D2310 " --> pdb=" O THR D2306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2317 Processing helix chain 'D' and resid 2318 through 2336 Processing helix chain 'D' and resid 2337 through 2353 removed outlier: 4.709A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU D2353 " --> pdb=" O ILE D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2364 removed outlier: 3.579A pdb=" N SER D2361 " --> pdb=" O ASN D2357 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2390 Processing helix chain 'D' and resid 2457 through 2472 removed outlier: 3.952A pdb=" N LEU D2470 " --> pdb=" O MET D2466 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG D2471 " --> pdb=" O ASN D2467 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2481 removed outlier: 4.362A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2537 removed outlier: 3.965A pdb=" N ILE D2512 " --> pdb=" O VAL D2508 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2550 removed outlier: 4.162A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP D2549 " --> pdb=" O ARG D2545 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASN D2550 " --> pdb=" O ASP D2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2544 through 2550' Processing helix chain 'D' and resid 2554 through 2561 Processing helix chain 'D' and resid 2564 through 2578 Processing helix chain 'D' and resid 2584 through 2597 Processing helix chain 'D' and resid 2607 through 2612 Processing sheet with id= 1, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= 2, first strand: chain 'A' and resid 252 through 255 Processing sheet with id= 3, first strand: chain 'A' and resid 284 through 288 removed outlier: 5.093A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 13.616A pdb=" N TYR A 304 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ALA A 317 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE A 306 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 313 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 368 through 371 Processing sheet with id= 5, first strand: chain 'A' and resid 396 through 401 removed outlier: 3.878A pdb=" N MET A 416 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 667 through 672 removed outlier: 4.167A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 800 through 803 Processing sheet with id= 8, first strand: chain 'A' and resid 2122 through 2128 removed outlier: 4.274A pdb=" N SER A2132 " --> pdb=" O ARG A2128 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 2395 through 2399 removed outlier: 7.316A pdb=" N PHE A2395 " --> pdb=" O ALA A2454 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER A2450 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 261 through 265 removed outlier: 5.276A pdb=" N LEU B 243 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N CYS B 254 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 13.968A pdb=" N VAL B 241 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 284 through 288 removed outlier: 5.157A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 13.966A pdb=" N TYR B 304 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N ALA B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 306 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 313 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS B 351 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 368 through 371 Processing sheet with id= 13, first strand: chain 'B' and resid 396 through 402 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'B' and resid 667 through 672 Processing sheet with id= 15, first strand: chain 'B' and resid 2122 through 2128 removed outlier: 4.214A pdb=" N SER B2132 " --> pdb=" O ARG B2128 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 261 through 265 removed outlier: 5.030A pdb=" N LEU C 243 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N CYS C 254 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 13.467A pdb=" N VAL C 241 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 244 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 284 through 288 removed outlier: 5.204A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'C' and resid 315 through 320 removed outlier: 5.402A pdb=" N LYS C 351 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 368 through 371 Processing sheet with id= 20, first strand: chain 'C' and resid 396 through 401 removed outlier: 4.132A pdb=" N MET C 416 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 667 through 672 removed outlier: 4.073A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 800 through 803 removed outlier: 4.290A pdb=" N TRP C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 2122 through 2128 removed outlier: 4.260A pdb=" N SER C2132 " --> pdb=" O ARG C2128 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 252 through 255 Processing sheet with id= 25, first strand: chain 'D' and resid 312 through 315 removed outlier: 4.453A pdb=" N ASN D 313 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N PHE D 306 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 288 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 309 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU D 282 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 368 through 371 Processing sheet with id= 27, first strand: chain 'D' and resid 396 through 401 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'D' and resid 667 through 672 removed outlier: 4.077A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 800 through 803 Processing sheet with id= 30, first strand: chain 'D' and resid 2122 through 2128 removed outlier: 4.341A pdb=" N SER D2132 " --> pdb=" O ARG D2128 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 2395 through 2399 removed outlier: 7.357A pdb=" N PHE D2395 " --> pdb=" O ALA D2454 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER D2450 " --> pdb=" O VAL D2399 " (cutoff:3.500A) 4144 hydrogen bonds defined for protein. 12378 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: 57.26 Time building geometry restraints manager: 86.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 65209 1.03 - 1.23: 1171 1.23 - 1.43: 26252 1.43 - 1.63: 38321 1.63 - 1.82: 681 Bond restraints: 131634 Sorted by residual: bond pdb=" CD1 TYR D 557 " pdb=" CE1 TYR D 557 " ideal model delta sigma weight residual 1.382 1.341 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CA VAL C1333 " pdb=" CB VAL C1333 " ideal model delta sigma weight residual 1.527 1.543 -0.017 1.31e-02 5.83e+03 1.61e+00 bond pdb=" C LEU B1391 " pdb=" N PRO B1392 " ideal model delta sigma weight residual 1.329 1.345 -0.015 1.22e-02 6.72e+03 1.58e+00 bond pdb=" CA VAL A1333 " pdb=" CB VAL A1333 " ideal model delta sigma weight residual 1.527 1.542 -0.016 1.31e-02 5.83e+03 1.41e+00 bond pdb=" CB GLU C1799 " pdb=" CG GLU C1799 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 131629 not shown) Histogram of bond angle deviations from ideal: 98.99 - 107.16: 2959 107.16 - 115.34: 166508 115.34 - 123.52: 57970 123.52 - 131.69: 10622 131.69 - 139.87: 83 Bond angle restraints: 238142 Sorted by residual: angle pdb=" CB MET B 497 " pdb=" CG MET B 497 " pdb=" SD MET B 497 " ideal model delta sigma weight residual 112.70 122.14 -9.44 3.00e+00 1.11e-01 9.89e+00 angle pdb=" CA GLY B1186 " pdb=" C GLY B1186 " pdb=" O GLY B1186 " ideal model delta sigma weight residual 122.24 119.65 2.59 8.70e-01 1.32e+00 8.84e+00 angle pdb=" CA LYS A1123 " pdb=" C LYS A1123 " pdb=" N SER A1124 " ideal model delta sigma weight residual 117.92 113.92 4.00 1.35e+00 5.49e-01 8.79e+00 angle pdb=" CB MET A1542 " pdb=" CG MET A1542 " pdb=" SD MET A1542 " ideal model delta sigma weight residual 112.70 121.57 -8.87 3.00e+00 1.11e-01 8.74e+00 angle pdb=" CB LYS C1594 " pdb=" CG LYS C1594 " pdb=" CD LYS C1594 " ideal model delta sigma weight residual 111.30 117.72 -6.42 2.30e+00 1.89e-01 7.80e+00 ... (remaining 238137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 57190 24.41 - 48.83: 3430 48.83 - 73.24: 814 73.24 - 97.66: 75 97.66 - 122.07: 16 Dihedral angle restraints: 61525 sinusoidal: 33807 harmonic: 27718 Sorted by residual: dihedral pdb=" CA TRP D1513 " pdb=" C TRP D1513 " pdb=" N LEU D1514 " pdb=" CA LEU D1514 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" C4 I3P C3002 " pdb=" C2 I3P C3002 " pdb=" C3 I3P C3002 " pdb=" O2 I3P C3002 " ideal model delta sinusoidal sigma weight residual 65.28 -172.65 -122.07 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1 I3P C3002 " pdb=" C2 I3P C3002 " pdb=" C3 I3P C3002 " pdb=" C4 I3P C3002 " ideal model delta sinusoidal sigma weight residual 56.81 -65.15 121.96 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 61522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 9138 0.057 - 0.115: 1075 0.115 - 0.172: 72 0.172 - 0.230: 3 0.230 - 0.287: 9 Chirality restraints: 10297 Sorted by residual: chirality pdb=" C2' ATP D3004 " pdb=" C1' ATP D3004 " pdb=" C3' ATP D3004 " pdb=" O2' ATP D3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C2' ATP C3004 " pdb=" C1' ATP C3004 " pdb=" C3' ATP C3004 " pdb=" O2' ATP C3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' ATP A3004 " pdb=" C2' ATP A3004 " pdb=" C4' ATP A3004 " pdb=" O3' ATP A3004 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 10294 not shown) Planarity restraints: 19076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 806 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO B 807 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 807 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 807 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1127 " -0.020 2.00e-02 2.50e+03 1.39e-02 7.74e+00 pdb=" CG TRP A1127 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A1127 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A1127 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1127 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A1127 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1127 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1127 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1127 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A1127 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP A1127 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP A1127 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A1127 " 0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A1127 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A1127 " -0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A1127 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1107 " 0.019 2.00e-02 2.50e+03 1.44e-02 6.18e+00 pdb=" CG TYR C1107 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR C1107 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C1107 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C1107 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C1107 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C1107 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C1107 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR C1107 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR C1107 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR C1107 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR C1107 " 0.001 2.00e-02 2.50e+03 ... (remaining 19073 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1950 2.08 - 2.71: 219897 2.71 - 3.34: 403472 3.34 - 3.97: 481410 3.97 - 4.60: 758880 Nonbonded interactions: 1865609 Sorted by model distance: nonbonded pdb=" OE1 GLN A1298 " pdb=" H GLN A1298 " model vdw 1.452 1.850 nonbonded pdb=" OE1 GLN B1188 " pdb=" H GLN B1188 " model vdw 1.488 1.850 nonbonded pdb=" OE1 GLU B 854 " pdb=" H GLU B 854 " model vdw 1.496 1.850 nonbonded pdb=" OE1 GLU C2011 " pdb=" H GLU C2011 " model vdw 1.524 1.850 nonbonded pdb=" O TYR B2117 " pdb=" HG1 THR B2121 " model vdw 1.538 1.850 ... (remaining 1865604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 235 through 672 or (resid 673 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or resid 689 through 1696 or \ resid 1718 through 2612 or resid 3001 through 3004)) selection = (chain 'B' and (resid 235 through 672 or (resid 673 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or resid 689 through 2612 or \ resid 3001 through 3004)) selection = (chain 'C' and (resid 235 through 673 or (resid 689 and (name N or name CA or na \ me C or name O or name CB or name HA )) or resid 690 through 1037 or (resid 1043 \ and (name N or name CA or name C or name O or name CB or name OG or name HA or \ name HB2 or name HB3 or name HG )) or resid 1044 through 1696 or resid 1718 thro \ ugh 2612 or resid 3001 through 3004)) selection = (chain 'D' and (resid 235 through 672 or (resid 673 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or resid 689 through 1004 or \ (resid 1022 and (name N or name CA or name C or name O or name CB or name HA )) \ or resid 1023 through 1557 or (resid 1586 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or n \ ame CE3 or name CZ2 or name CZ3 or name CH2 or name HA or name HB2 or name HB3 o \ r name HD1 or name HE1 or name HE3 or name HZ2 or name HZ3 or name HH2)) or resi \ d 1587 through 1696 or resid 1718 through 2612 or resid 3001 through 3004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.420 Extract box with map and model: 29.650 Check model and map are aligned: 1.410 Set scattering table: 0.910 Process input model: 393.910 Find NCS groups from input model: 6.840 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 441.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 66276 Z= 0.151 Angle : 0.517 9.436 89591 Z= 0.284 Chirality : 0.035 0.287 10297 Planarity : 0.003 0.071 11335 Dihedral : 17.374 122.074 25001 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.49 % Favored : 98.50 % Rotamer: Outliers : 0.39 % Allowed : 15.39 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.09), residues: 7909 helix: 2.71 (0.07), residues: 5480 sheet: -0.01 (0.23), residues: 475 loop : 0.57 (0.15), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A1127 HIS 0.007 0.001 HIS A1203 PHE 0.020 0.001 PHE C1235 TYR 0.043 0.001 TYR C1107 ARG 0.011 0.000 ARG C2131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1218 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1190 time to evaluate : 7.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 610 ILE cc_start: -0.4037 (OUTLIER) cc_final: -0.4405 (tp) REVERT: A 834 MET cc_start: -0.2894 (mtp) cc_final: -0.4010 (ttm) REVERT: A 1105 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8489 (tm-30) REVERT: A 1363 MET cc_start: 0.6601 (tpt) cc_final: 0.5641 (tpp) REVERT: A 1542 MET cc_start: 0.6061 (tpp) cc_final: 0.5785 (tpp) REVERT: A 2289 ASN cc_start: 0.7849 (t0) cc_final: 0.7645 (t0) REVERT: A 2318 MET cc_start: 0.8816 (mmt) cc_final: 0.8601 (ppp) REVERT: A 2326 TYR cc_start: 0.8135 (t80) cc_final: 0.7900 (t80) REVERT: B 416 MET cc_start: -0.0575 (ttt) cc_final: -0.0832 (ttm) REVERT: B 497 MET cc_start: 0.7195 (tpp) cc_final: 0.6937 (tpp) REVERT: B 1023 MET cc_start: -0.1947 (mmt) cc_final: -0.2841 (ttm) REVERT: B 1221 MET cc_start: -0.2904 (tpp) cc_final: -0.3249 (ttm) REVERT: B 1551 MET cc_start: 0.0512 (tpp) cc_final: -0.0754 (ttp) REVERT: C 552 MET cc_start: 0.0460 (ttp) cc_final: 0.0073 (tpp) REVERT: C 632 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7071 (t0) REVERT: C 1322 MET cc_start: -0.2095 (mmm) cc_final: -0.2776 (mmm) REVERT: C 1531 MET cc_start: 0.2907 (tpt) cc_final: 0.1776 (mmt) REVERT: C 1586 TRP cc_start: 0.1895 (m100) cc_final: -0.0935 (p-90) REVERT: C 2226 MET cc_start: 0.7340 (mmp) cc_final: 0.7071 (mtm) REVERT: C 2318 MET cc_start: 0.8745 (mmm) cc_final: 0.8489 (ppp) REVERT: D 580 MET cc_start: 0.7758 (ppp) cc_final: 0.7492 (tmm) REVERT: D 1903 LEU cc_start: 0.8487 (mt) cc_final: 0.8214 (mt) REVERT: D 2181 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7504 (tm-30) outliers start: 28 outliers final: 9 residues processed: 1211 average time/residue: 1.6789 time to fit residues: 3312.1312 Evaluate side-chains 753 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 742 time to evaluate : 7.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 1203 HIS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain D residue 832 ASN Chi-restraints excluded: chain D residue 1685 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 674 optimal weight: 10.0000 chunk 605 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 206 optimal weight: 50.0000 chunk 408 optimal weight: 20.0000 chunk 323 optimal weight: 20.0000 chunk 626 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 chunk 380 optimal weight: 9.9990 chunk 466 optimal weight: 10.0000 chunk 725 optimal weight: 9.9990 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN A1102 GLN ** A1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1636 GLN A1883 ASN A1956 GLN ** A2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2467 ASN ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1884 HIS ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2161 GLN B2179 HIS ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2303 ASN ** B2468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN C 721 HIS ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1798 GLN ** C1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 ASN C2292 ASN C2357 ASN C2579 ASN C2598 ASN D 625 ASN D1168 ASN ** D1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1285 HIS D1327 ASN D1565 ASN D1649 GLN ** D1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2179 HIS D2467 ASN D2510 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 66276 Z= 0.525 Angle : 0.761 11.366 89591 Z= 0.418 Chirality : 0.041 0.234 10297 Planarity : 0.005 0.082 11335 Dihedral : 7.197 87.804 8921 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.30 % Favored : 97.69 % Rotamer: Outliers : 2.48 % Allowed : 17.26 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 7909 helix: 1.34 (0.07), residues: 5522 sheet: -0.10 (0.23), residues: 464 loop : -0.12 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A2184 HIS 0.016 0.002 HIS C2558 PHE 0.034 0.002 PHE A2222 TYR 0.022 0.002 TYR A1928 ARG 0.016 0.001 ARG B2200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 808 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 628 time to evaluate : 7.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.1351 (mmp) cc_final: 0.0957 (mmp) REVERT: A 539 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6559 (mm-30) REVERT: A 798 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.5680 (tppt) REVERT: A 834 MET cc_start: -0.3130 (mtp) cc_final: -0.3475 (ttm) REVERT: A 1105 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8546 (tm-30) REVERT: A 1363 MET cc_start: 0.6656 (tpt) cc_final: 0.5705 (tpp) REVERT: A 1542 MET cc_start: 0.6262 (tpp) cc_final: 0.6043 (tpp) REVERT: A 1603 GLU cc_start: 0.5986 (tp30) cc_final: 0.5715 (tp30) REVERT: B 416 MET cc_start: -0.0285 (ttt) cc_final: -0.0509 (ttm) REVERT: B 497 MET cc_start: 0.7551 (tpp) cc_final: 0.7350 (tpp) REVERT: B 1023 MET cc_start: -0.1122 (mmt) cc_final: -0.2372 (ttm) REVERT: B 1221 MET cc_start: -0.1953 (tpp) cc_final: -0.2437 (ttm) REVERT: B 1348 MET cc_start: 0.2197 (ptp) cc_final: 0.1818 (ptm) REVERT: B 2316 MET cc_start: 0.8763 (mmt) cc_final: 0.8560 (mmt) REVERT: C 552 MET cc_start: 0.0993 (ttp) cc_final: 0.0317 (tpp) REVERT: C 1322 MET cc_start: -0.2162 (mmm) cc_final: -0.3026 (mmm) REVERT: C 1531 MET cc_start: 0.2893 (tpt) cc_final: 0.1777 (mmt) REVERT: C 2188 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9261 (mt) REVERT: C 2553 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9067 (m) REVERT: D 580 MET cc_start: 0.7887 (ppp) cc_final: 0.7507 (tmm) REVERT: D 2133 MET cc_start: 0.8370 (mtp) cc_final: 0.8163 (mtp) outliers start: 180 outliers final: 103 residues processed: 781 average time/residue: 1.5187 time to fit residues: 1935.0237 Evaluate side-chains 670 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 564 time to evaluate : 7.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 1203 HIS Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1250 LEU Chi-restraints excluded: chain B residue 1604 GLU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1718 TRP Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2122 SER Chi-restraints excluded: chain B residue 2190 SER Chi-restraints excluded: chain B residue 2198 SER Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2497 ASP Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain B residue 2552 THR Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 816 ASP Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 987 ILE Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1325 LEU Chi-restraints excluded: chain C residue 1602 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1896 ASN Chi-restraints excluded: chain C residue 1954 GLU Chi-restraints excluded: chain C residue 1963 GLU Chi-restraints excluded: chain C residue 2118 GLU Chi-restraints excluded: chain C residue 2188 LEU Chi-restraints excluded: chain C residue 2201 MET Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain C residue 2596 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 611 THR Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 978 ILE Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1083 SER Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1115 ASP Chi-restraints excluded: chain D residue 1188 GLN Chi-restraints excluded: chain D residue 1319 ASP Chi-restraints excluded: chain D residue 1346 LEU Chi-restraints excluded: chain D residue 1347 ASP Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1448 MET Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1547 HIS Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1731 GLU Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1787 LYS Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2150 GLU Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2272 SER Chi-restraints excluded: chain D residue 2384 SER Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2449 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2479 ILE Chi-restraints excluded: chain D residue 2526 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 403 optimal weight: 50.0000 chunk 225 optimal weight: 40.0000 chunk 603 optimal weight: 40.0000 chunk 494 optimal weight: 20.0000 chunk 200 optimal weight: 40.0000 chunk 726 optimal weight: 10.0000 chunk 785 optimal weight: 0.9990 chunk 647 optimal weight: 0.9990 chunk 720 optimal weight: 8.9990 chunk 247 optimal weight: 50.0000 chunk 583 optimal weight: 0.7980 overall best weight: 4.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 HIS ** A1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1896 ASN ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 GLN ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1266 HIS ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1596 GLN ** C1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2592 GLN C2598 ASN D 641 ASN D1193 GLN D1239 ASN D1266 HIS ** D1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1590 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 66276 Z= 0.235 Angle : 0.532 7.556 89591 Z= 0.288 Chirality : 0.035 0.172 10297 Planarity : 0.003 0.042 11335 Dihedral : 5.715 89.766 8906 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.99 % Favored : 98.00 % Rotamer: Outliers : 1.88 % Allowed : 17.59 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.09), residues: 7909 helix: 1.99 (0.07), residues: 5532 sheet: -0.05 (0.23), residues: 464 loop : 0.12 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2184 HIS 0.010 0.001 HIS C1247 PHE 0.015 0.001 PHE C1092 TYR 0.019 0.001 TYR C1107 ARG 0.012 0.000 ARG B 709 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 738 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 601 time to evaluate : 7.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 MET cc_start: 0.6217 (pmm) cc_final: 0.5934 (pmm) REVERT: A 539 GLU cc_start: 0.6411 (mm-30) cc_final: 0.6044 (mm-30) REVERT: A 834 MET cc_start: -0.3264 (mtp) cc_final: -0.3652 (ttm) REVERT: A 1105 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8560 (tm-30) REVERT: A 1363 MET cc_start: 0.6596 (tpt) cc_final: 0.5647 (tpp) REVERT: A 2326 TYR cc_start: 0.8352 (t80) cc_final: 0.7900 (t80) REVERT: B 416 MET cc_start: -0.0473 (ttt) cc_final: -0.0696 (ttm) REVERT: B 764 MET cc_start: 0.1599 (mtp) cc_final: 0.1371 (mtp) REVERT: B 1023 MET cc_start: -0.1160 (mmt) cc_final: -0.2358 (ttm) REVERT: B 1221 MET cc_start: -0.1902 (tpp) cc_final: -0.2475 (ttm) REVERT: B 1348 MET cc_start: 0.2203 (ptp) cc_final: 0.1964 (ptm) REVERT: B 2316 MET cc_start: 0.8771 (mmt) cc_final: 0.8450 (mmt) REVERT: C 1111 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8138 (tptp) REVERT: C 1316 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8075 (pttm) REVERT: C 1322 MET cc_start: -0.2197 (mmm) cc_final: -0.3295 (mmm) REVERT: C 1363 MET cc_start: 0.4604 (mmm) cc_final: 0.4400 (mmm) REVERT: C 1531 MET cc_start: 0.3002 (tpt) cc_final: 0.1898 (mmt) REVERT: C 2226 MET cc_start: 0.7766 (mmp) cc_final: 0.7380 (mtm) REVERT: D 580 MET cc_start: 0.7911 (ppp) cc_final: 0.7606 (tmm) REVERT: D 1914 MET cc_start: 0.8646 (tpp) cc_final: 0.8438 (tpp) outliers start: 137 outliers final: 96 residues processed: 710 average time/residue: 1.4820 time to fit residues: 1712.7923 Evaluate side-chains 656 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 559 time to evaluate : 7.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1490 SER Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1250 LEU Chi-restraints excluded: chain B residue 1402 HIS Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1896 ASN Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2198 SER Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1107 TYR Chi-restraints excluded: chain C residue 1316 LYS Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1896 ASN Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain C residue 2592 GLN Chi-restraints excluded: chain D residue 611 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 832 ASN Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 978 ILE Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1083 SER Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1346 LEU Chi-restraints excluded: chain D residue 1432 TYR Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1547 HIS Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1672 MET Chi-restraints excluded: chain D residue 1731 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1780 LYS Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 2150 GLU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2384 SER Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2526 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 718 optimal weight: 5.9990 chunk 546 optimal weight: 5.9990 chunk 377 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 488 optimal weight: 20.0000 chunk 729 optimal weight: 3.9990 chunk 772 optimal weight: 5.9990 chunk 381 optimal weight: 0.9990 chunk 691 optimal weight: 7.9990 chunk 208 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2592 GLN D 641 ASN ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 HIS D1995 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 66276 Z= 0.236 Angle : 0.519 9.284 89591 Z= 0.281 Chirality : 0.035 0.213 10297 Planarity : 0.003 0.040 11335 Dihedral : 5.312 88.818 8902 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 17.51 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.09), residues: 7909 helix: 2.13 (0.07), residues: 5524 sheet: -0.08 (0.23), residues: 466 loop : 0.18 (0.15), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2184 HIS 0.019 0.001 HIS C1247 PHE 0.020 0.001 PHE C1092 TYR 0.018 0.001 TYR C1107 ARG 0.016 0.000 ARG C 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 720 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 574 time to evaluate : 7.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 798 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.5852 (tppt) REVERT: A 834 MET cc_start: -0.3200 (mtp) cc_final: -0.3527 (ttm) REVERT: A 1105 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8548 (tm-30) REVERT: B 416 MET cc_start: -0.0512 (ttt) cc_final: -0.0744 (ttm) REVERT: B 764 MET cc_start: 0.1506 (mtp) cc_final: 0.1263 (mtp) REVERT: B 2316 MET cc_start: 0.8898 (mmt) cc_final: 0.8668 (mmt) REVERT: C 1111 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8165 (tptp) REVERT: C 1316 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8139 (pttm) REVERT: C 1322 MET cc_start: -0.2224 (mmm) cc_final: -0.2962 (mmm) REVERT: C 1531 MET cc_start: 0.2929 (tpt) cc_final: 0.1833 (mmt) REVERT: C 2226 MET cc_start: 0.7873 (mmp) cc_final: 0.7460 (mtm) REVERT: D 580 MET cc_start: 0.7887 (ppp) cc_final: 0.7571 (tmm) REVERT: D 1735 LYS cc_start: 0.8642 (tppt) cc_final: 0.8442 (tptm) REVERT: D 1739 ASP cc_start: 0.8035 (m-30) cc_final: 0.7750 (m-30) outliers start: 146 outliers final: 111 residues processed: 693 average time/residue: 1.6541 time to fit residues: 1889.0299 Evaluate side-chains 658 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 545 time to evaluate : 7.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1250 LEU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2198 SER Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 543 ASP Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1316 LYS Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1657 SER Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1896 ASN Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1991 GLN Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain C residue 2582 ASP Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 THR Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 894 CYS Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1346 LEU Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1432 TYR Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1547 HIS Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1731 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1780 LYS Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1867 VAL Chi-restraints excluded: chain D residue 2014 GLU Chi-restraints excluded: chain D residue 2150 GLU Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2384 SER Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2526 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 643 optimal weight: 10.0000 chunk 438 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 575 optimal weight: 0.3980 chunk 318 optimal weight: 40.0000 chunk 659 optimal weight: 5.9990 chunk 533 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 394 optimal weight: 4.9990 chunk 693 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1797 GLN A1965 ASN A2550 ASN ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 ASN ** B 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1953 HIS ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1168 ASN C1436 HIS ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1965 ASN D 384 ASN D 783 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 66276 Z= 0.258 Angle : 0.528 11.372 89591 Z= 0.286 Chirality : 0.035 0.148 10297 Planarity : 0.003 0.037 11335 Dihedral : 5.201 88.466 8902 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 2.24 % Allowed : 17.16 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.09), residues: 7909 helix: 2.11 (0.07), residues: 5515 sheet: -0.09 (0.23), residues: 464 loop : 0.16 (0.15), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2184 HIS 0.024 0.001 HIS C1247 PHE 0.027 0.001 PHE B1772 TYR 0.021 0.001 TYR C1107 ARG 0.004 0.000 ARG B2200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 729 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 566 time to evaluate : 9.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: -0.3018 (mtp) cc_final: -0.3365 (ttm) REVERT: A 1105 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8528 (tm-30) REVERT: B 416 MET cc_start: -0.0509 (ttt) cc_final: -0.0747 (ttm) REVERT: B 764 MET cc_start: 0.1509 (mtp) cc_final: 0.1257 (mtp) REVERT: B 1782 SER cc_start: 0.2962 (OUTLIER) cc_final: 0.1992 (p) REVERT: B 2316 MET cc_start: 0.8990 (mmt) cc_final: 0.8671 (mmt) REVERT: C 552 MET cc_start: 0.0838 (ttp) cc_final: 0.0139 (tpt) REVERT: C 1044 MET cc_start: 0.5135 (ptp) cc_final: 0.4650 (ptt) REVERT: C 1111 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8235 (tptp) REVERT: C 1320 MET cc_start: 0.3706 (mtp) cc_final: 0.3473 (mtp) REVERT: C 1322 MET cc_start: -0.2139 (mmm) cc_final: -0.2800 (mmm) REVERT: C 1531 MET cc_start: 0.3047 (tpt) cc_final: 0.1983 (mmt) REVERT: C 2226 MET cc_start: 0.7926 (mmp) cc_final: 0.7584 (mtm) REVERT: D 580 MET cc_start: 0.7877 (ppp) cc_final: 0.7568 (tmm) outliers start: 163 outliers final: 127 residues processed: 695 average time/residue: 1.4199 time to fit residues: 1621.5449 Evaluate side-chains 666 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 538 time to evaluate : 8.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1782 SER Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2056 LEU Chi-restraints excluded: chain B residue 2122 SER Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2198 SER Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2484 SER Chi-restraints excluded: chain B residue 2497 ASP Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2552 THR Chi-restraints excluded: chain B residue 2579 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 543 ASP Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1250 LEU Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1657 SER Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1896 ASN Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1954 GLU Chi-restraints excluded: chain C residue 1991 GLN Chi-restraints excluded: chain C residue 2207 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain C residue 2582 ASP Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 642 HIS Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1346 LEU Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1547 HIS Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1672 MET Chi-restraints excluded: chain D residue 1679 TYR Chi-restraints excluded: chain D residue 1731 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1780 LYS Chi-restraints excluded: chain D residue 1801 LYS Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1867 VAL Chi-restraints excluded: chain D residue 1892 LEU Chi-restraints excluded: chain D residue 2014 GLU Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2150 GLU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2384 SER Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2532 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 259 optimal weight: 30.0000 chunk 695 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 453 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 773 optimal weight: 5.9990 chunk 641 optimal weight: 9.9990 chunk 357 optimal weight: 3.9990 chunk 64 optimal weight: 40.0000 chunk 255 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 GLN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 GLN ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1515 GLN D1563 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 66276 Z= 0.258 Angle : 0.523 10.278 89591 Z= 0.284 Chirality : 0.035 0.213 10297 Planarity : 0.003 0.039 11335 Dihedral : 5.159 89.362 8902 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.40 % Rotamer: Outliers : 2.15 % Allowed : 17.48 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.09), residues: 7909 helix: 2.11 (0.07), residues: 5524 sheet: -0.12 (0.23), residues: 470 loop : 0.15 (0.15), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2184 HIS 0.018 0.001 HIS C1247 PHE 0.023 0.001 PHE B1786 TYR 0.019 0.001 TYR C1107 ARG 0.021 0.000 ARG A2021 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 693 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 537 time to evaluate : 7.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: -0.3003 (mtp) cc_final: -0.3394 (ttm) REVERT: A 1105 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8540 (tm-30) REVERT: B 416 MET cc_start: -0.0453 (ttt) cc_final: -0.0690 (ttm) REVERT: B 764 MET cc_start: 0.1619 (mtp) cc_final: 0.1387 (mtp) REVERT: B 1293 HIS cc_start: -0.0497 (OUTLIER) cc_final: -0.1409 (m170) REVERT: C 552 MET cc_start: 0.0764 (ttp) cc_final: 0.0158 (tpp) REVERT: C 1044 MET cc_start: 0.5200 (ptp) cc_final: 0.4791 (ptt) REVERT: C 1111 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8254 (tptp) REVERT: C 1322 MET cc_start: -0.2069 (mmm) cc_final: -0.2735 (mmm) REVERT: C 1508 LEU cc_start: 0.2122 (OUTLIER) cc_final: 0.1769 (tp) REVERT: C 1531 MET cc_start: 0.3049 (tpt) cc_final: 0.1981 (mmt) REVERT: C 1776 MET cc_start: 0.7237 (mpp) cc_final: 0.6871 (mtm) REVERT: C 2226 MET cc_start: 0.7925 (mmp) cc_final: 0.7622 (mtm) REVERT: D 580 MET cc_start: 0.7915 (ppp) cc_final: 0.7653 (tmm) REVERT: D 702 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7556 (mm-30) outliers start: 156 outliers final: 127 residues processed: 667 average time/residue: 1.5858 time to fit residues: 1750.5735 Evaluate side-chains 655 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 526 time to evaluate : 7.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 976 GLN Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1065 HIS Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1250 LEU Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2056 LEU Chi-restraints excluded: chain B residue 2122 SER Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2198 SER Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2484 SER Chi-restraints excluded: chain B residue 2497 ASP Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2552 THR Chi-restraints excluded: chain B residue 2579 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 543 ASP Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1508 LEU Chi-restraints excluded: chain C residue 1657 SER Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1896 ASN Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1954 GLU Chi-restraints excluded: chain C residue 1991 GLN Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain C residue 2582 ASP Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1346 LEU Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1547 HIS Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1679 TYR Chi-restraints excluded: chain D residue 1731 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1780 LYS Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1867 VAL Chi-restraints excluded: chain D residue 1887 ASP Chi-restraints excluded: chain D residue 2014 GLU Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2150 GLU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2272 SER Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2384 SER Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2532 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 745 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 440 optimal weight: 10.0000 chunk 564 optimal weight: 0.9990 chunk 437 optimal weight: 9.9990 chunk 650 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 chunk 770 optimal weight: 4.9990 chunk 481 optimal weight: 8.9990 chunk 469 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 HIS ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 GLN ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1170 GLN ** D1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 66276 Z= 0.260 Angle : 0.522 9.355 89591 Z= 0.283 Chirality : 0.035 0.193 10297 Planarity : 0.003 0.041 11335 Dihedral : 5.104 89.616 8902 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 2.20 % Allowed : 17.54 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.09), residues: 7909 helix: 2.11 (0.07), residues: 5530 sheet: -0.08 (0.24), residues: 457 loop : 0.10 (0.15), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2184 HIS 0.031 0.001 HIS C1773 PHE 0.019 0.001 PHE A1082 TYR 0.019 0.001 TYR C1107 ARG 0.008 0.000 ARG A2021 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 697 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 537 time to evaluate : 7.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: -0.2996 (mtp) cc_final: -0.3488 (ttm) REVERT: A 1105 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8579 (tm-30) REVERT: B 416 MET cc_start: -0.0434 (ttt) cc_final: -0.0675 (ttm) REVERT: B 764 MET cc_start: 0.1631 (mtp) cc_final: 0.1403 (mtp) REVERT: B 1293 HIS cc_start: -0.0408 (OUTLIER) cc_final: -0.2303 (m170) REVERT: C 552 MET cc_start: 0.0713 (ttp) cc_final: 0.0120 (tpp) REVERT: C 1044 MET cc_start: 0.5210 (ptp) cc_final: 0.4769 (ptt) REVERT: C 1111 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8281 (tptp) REVERT: C 1322 MET cc_start: -0.1919 (mmm) cc_final: -0.2609 (mmm) REVERT: C 1531 MET cc_start: 0.2906 (tpt) cc_final: 0.1543 (mtt) REVERT: C 2226 MET cc_start: 0.7928 (mmp) cc_final: 0.7664 (mtm) REVERT: D 580 MET cc_start: 0.7965 (ppp) cc_final: 0.7740 (tmm) REVERT: D 702 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7627 (mm-30) REVERT: D 2605 MET cc_start: 0.8808 (mmm) cc_final: 0.8566 (mmp) outliers start: 160 outliers final: 138 residues processed: 673 average time/residue: 1.5077 time to fit residues: 1670.0354 Evaluate side-chains 657 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 518 time to evaluate : 7.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 976 GLN Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1250 LEU Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2056 LEU Chi-restraints excluded: chain B residue 2122 SER Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2198 SER Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2484 SER Chi-restraints excluded: chain B residue 2497 ASP Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2536 THR Chi-restraints excluded: chain B residue 2552 THR Chi-restraints excluded: chain B residue 2579 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 543 ASP Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1091 THR Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1250 LEU Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1657 SER Chi-restraints excluded: chain C residue 1673 LEU Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1896 ASN Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1954 GLU Chi-restraints excluded: chain C residue 1991 GLN Chi-restraints excluded: chain C residue 2061 SER Chi-restraints excluded: chain C residue 2207 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain C residue 2582 ASP Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 971 ILE Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1346 LEU Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1547 HIS Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1679 TYR Chi-restraints excluded: chain D residue 1731 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1867 VAL Chi-restraints excluded: chain D residue 1887 ASP Chi-restraints excluded: chain D residue 2014 GLU Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2150 GLU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2384 SER Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2532 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 476 optimal weight: 10.0000 chunk 307 optimal weight: 40.0000 chunk 459 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 489 optimal weight: 40.0000 chunk 524 optimal weight: 7.9990 chunk 380 optimal weight: 10.0000 chunk 71 optimal weight: 40.0000 chunk 605 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A1265 GLN A1285 HIS ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1380 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1798 GLN ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1897 ASN ** D 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 66276 Z= 0.456 Angle : 0.650 8.468 89591 Z= 0.365 Chirality : 0.038 0.200 10297 Planarity : 0.004 0.048 11335 Dihedral : 5.409 84.702 8902 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 2.71 % Allowed : 17.60 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.09), residues: 7909 helix: 1.29 (0.07), residues: 5524 sheet: -0.33 (0.24), residues: 434 loop : -0.39 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D1127 HIS 0.013 0.002 HIS B2558 PHE 0.028 0.002 PHE D 761 TYR 0.019 0.002 TYR B1928 ARG 0.008 0.001 ARG D2200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 698 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 501 time to evaluate : 7.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ILE cc_start: -0.3829 (OUTLIER) cc_final: -0.4294 (tp) REVERT: A 834 MET cc_start: -0.2903 (mtp) cc_final: -0.3443 (ttm) REVERT: A 1105 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8657 (tm-30) REVERT: B 416 MET cc_start: -0.0296 (ttt) cc_final: -0.0534 (ttm) REVERT: B 764 MET cc_start: 0.1837 (mtp) cc_final: 0.1595 (mtp) REVERT: B 1023 MET cc_start: -0.0854 (mmt) cc_final: -0.1113 (mmt) REVERT: B 1293 HIS cc_start: -0.0611 (OUTLIER) cc_final: -0.2539 (m170) REVERT: C 1044 MET cc_start: 0.5837 (ptp) cc_final: 0.5357 (ptt) REVERT: C 1111 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8422 (tptp) REVERT: C 1182 MET cc_start: 0.1457 (OUTLIER) cc_final: 0.1252 (ttt) REVERT: C 1320 MET cc_start: 0.4054 (mtp) cc_final: 0.3839 (mtp) REVERT: C 1322 MET cc_start: -0.1633 (mmm) cc_final: -0.2423 (mmm) REVERT: C 1531 MET cc_start: 0.2780 (tpt) cc_final: 0.1397 (mtt) REVERT: D 580 MET cc_start: 0.8010 (ppp) cc_final: 0.7802 (tmm) REVERT: D 702 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7685 (mm-30) outliers start: 197 outliers final: 161 residues processed: 659 average time/residue: 1.6106 time to fit residues: 1773.0264 Evaluate side-chains 643 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 479 time to evaluate : 7.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1781 LYS Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2314 MET Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 489 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 976 GLN Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1250 LEU Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2025 LEU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2056 LEU Chi-restraints excluded: chain B residue 2122 SER Chi-restraints excluded: chain B residue 2198 SER Chi-restraints excluded: chain B residue 2225 TYR Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2484 SER Chi-restraints excluded: chain B residue 2497 ASP Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2536 THR Chi-restraints excluded: chain B residue 2552 THR Chi-restraints excluded: chain B residue 2579 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 994 PHE Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1078 LEU Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1182 MET Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1603 GLU Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1896 ASN Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1954 GLU Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1991 GLN Chi-restraints excluded: chain C residue 2118 GLU Chi-restraints excluded: chain C residue 2269 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2400 ASP Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2499 LEU Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain C residue 2582 ASP Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 THR Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 642 HIS Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 978 ILE Chi-restraints excluded: chain D residue 987 ILE Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1083 SER Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1252 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1301 ASP Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1547 HIS Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1607 LYS Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1655 MET Chi-restraints excluded: chain D residue 1679 TYR Chi-restraints excluded: chain D residue 1731 GLU Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1780 LYS Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1867 VAL Chi-restraints excluded: chain D residue 1887 ASP Chi-restraints excluded: chain D residue 2014 GLU Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2150 GLU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2272 SER Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2384 SER Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2503 ILE Chi-restraints excluded: chain D residue 2532 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 700 optimal weight: 7.9990 chunk 737 optimal weight: 3.9990 chunk 673 optimal weight: 9.9990 chunk 717 optimal weight: 3.9990 chunk 431 optimal weight: 20.0000 chunk 312 optimal weight: 50.0000 chunk 563 optimal weight: 1.9990 chunk 220 optimal weight: 0.0040 chunk 648 optimal weight: 0.3980 chunk 678 optimal weight: 5.9990 chunk 715 optimal weight: 3.9990 overall best weight: 2.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 GLN ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1798 GLN ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 GLN D1415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 66276 Z= 0.172 Angle : 0.515 12.391 89591 Z= 0.272 Chirality : 0.035 0.161 10297 Planarity : 0.003 0.050 11335 Dihedral : 5.160 89.683 8902 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 1.77 % Allowed : 18.54 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.09), residues: 7909 helix: 2.04 (0.07), residues: 5512 sheet: -0.20 (0.24), residues: 454 loop : 0.02 (0.15), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 696 HIS 0.010 0.001 HIS D1419 PHE 0.023 0.001 PHE D1480 TYR 0.018 0.001 TYR C1107 ARG 0.004 0.000 ARG D 743 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 674 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 545 time to evaluate : 7.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 ILE cc_start: -0.3885 (OUTLIER) cc_final: -0.4336 (tp) REVERT: A 834 MET cc_start: -0.3003 (mtp) cc_final: -0.3512 (ttm) REVERT: A 1105 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8589 (tm-30) REVERT: B 416 MET cc_start: -0.0370 (ttt) cc_final: -0.0604 (ttm) REVERT: B 764 MET cc_start: 0.1707 (mtp) cc_final: 0.1446 (mtp) REVERT: B 1023 MET cc_start: -0.1045 (mmt) cc_final: -0.1251 (mmt) REVERT: B 1293 HIS cc_start: -0.0426 (OUTLIER) cc_final: -0.2313 (m170) REVERT: B 2191 MET cc_start: 0.7407 (mmm) cc_final: 0.7090 (tpt) REVERT: B 2316 MET cc_start: 0.8960 (mmt) cc_final: 0.8704 (mmt) REVERT: C 1044 MET cc_start: 0.5770 (ptp) cc_final: 0.5424 (ptt) REVERT: C 1111 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8371 (tptp) REVERT: C 1322 MET cc_start: -0.1823 (mmm) cc_final: -0.2634 (mmm) REVERT: C 1531 MET cc_start: 0.2849 (tpt) cc_final: 0.1477 (mtt) REVERT: D 702 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 2608 MET cc_start: 0.7533 (mmm) cc_final: 0.7313 (mmt) outliers start: 129 outliers final: 117 residues processed: 646 average time/residue: 1.4609 time to fit residues: 1559.0125 Evaluate side-chains 630 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 511 time to evaluate : 7.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2182 MET Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 976 GLN Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1250 LEU Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1798 GLN Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2056 LEU Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2273 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2579 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1247 HIS Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1595 LEU Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1991 GLN Chi-restraints excluded: chain C residue 2207 ILE Chi-restraints excluded: chain C residue 2269 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 642 HIS Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 894 CYS Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1083 SER Chi-restraints excluded: chain D residue 1091 THR Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1602 LEU Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1867 VAL Chi-restraints excluded: chain D residue 2014 GLU Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2272 SER Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 471 optimal weight: 8.9990 chunk 758 optimal weight: 3.9990 chunk 463 optimal weight: 8.9990 chunk 359 optimal weight: 2.9990 chunk 527 optimal weight: 3.9990 chunk 796 optimal weight: 3.9990 chunk 732 optimal weight: 3.9990 chunk 633 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 489 optimal weight: 30.0000 chunk 388 optimal weight: 0.1980 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1443 ASN ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1419 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 66276 Z= 0.201 Angle : 0.520 11.262 89591 Z= 0.277 Chirality : 0.034 0.169 10297 Planarity : 0.003 0.040 11335 Dihedral : 5.084 89.363 8902 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 1.71 % Allowed : 18.69 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.09), residues: 7909 helix: 2.16 (0.07), residues: 5518 sheet: -0.20 (0.24), residues: 456 loop : 0.08 (0.15), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2184 HIS 0.008 0.001 HIS C1773 PHE 0.017 0.001 PHE C1910 TYR 0.018 0.001 TYR C1107 ARG 0.013 0.000 ARG C 738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15818 Ramachandran restraints generated. 7909 Oldfield, 0 Emsley, 7909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue SER 1042 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 639 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 515 time to evaluate : 8.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 MET cc_start: 0.0101 (ppp) cc_final: -0.1001 (ttp) REVERT: A 610 ILE cc_start: -0.3873 (OUTLIER) cc_final: -0.4320 (tp) REVERT: A 834 MET cc_start: -0.2964 (mtp) cc_final: -0.3461 (ttm) REVERT: A 1105 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8588 (tm-30) REVERT: B 416 MET cc_start: -0.0373 (ttt) cc_final: -0.0610 (ttm) REVERT: B 1023 MET cc_start: -0.0957 (mmt) cc_final: -0.1160 (mmt) REVERT: B 1293 HIS cc_start: -0.0422 (OUTLIER) cc_final: -0.2326 (m170) REVERT: B 2191 MET cc_start: 0.7391 (mmm) cc_final: 0.7052 (tpt) REVERT: B 2316 MET cc_start: 0.8956 (mmt) cc_final: 0.8718 (mmt) REVERT: C 1044 MET cc_start: 0.5760 (ptp) cc_final: 0.5294 (ptt) REVERT: C 1111 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8380 (tptp) REVERT: C 1322 MET cc_start: -0.1672 (mmm) cc_final: -0.2487 (mmm) REVERT: C 1531 MET cc_start: 0.2856 (tpt) cc_final: 0.1426 (mtt) REVERT: D 702 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7733 (mm-30) outliers start: 124 outliers final: 112 residues processed: 617 average time/residue: 1.5145 time to fit residues: 1547.6118 Evaluate side-chains 624 residues out of total 7292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 510 time to evaluate : 7.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 587 TYR Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1107 TYR Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1384 GLU Chi-restraints excluded: chain A residue 1492 GLN Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1781 LYS Chi-restraints excluded: chain A residue 2003 LEU Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2182 MET Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 816 ASP Chi-restraints excluded: chain B residue 1090 HIS Chi-restraints excluded: chain B residue 1236 CYS Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1729 ASP Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1798 GLN Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 2004 MET Chi-restraints excluded: chain B residue 2011 GLU Chi-restraints excluded: chain B residue 2019 SER Chi-restraints excluded: chain B residue 2048 GLU Chi-restraints excluded: chain B residue 2056 LEU Chi-restraints excluded: chain B residue 2269 ILE Chi-restraints excluded: chain B residue 2290 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2467 ASN Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2499 LEU Chi-restraints excluded: chain B residue 2536 THR Chi-restraints excluded: chain B residue 2579 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 779 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 836 PHE Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1079 PHE Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1691 LEU Chi-restraints excluded: chain C residue 1749 ILE Chi-restraints excluded: chain C residue 1750 PHE Chi-restraints excluded: chain C residue 1912 ASP Chi-restraints excluded: chain C residue 1974 ILE Chi-restraints excluded: chain C residue 1991 GLN Chi-restraints excluded: chain C residue 2269 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2553 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1018 SER Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1105 GLU Chi-restraints excluded: chain D residue 1181 LYS Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1381 VAL Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1551 MET Chi-restraints excluded: chain D residue 1603 GLU Chi-restraints excluded: chain D residue 1620 VAL Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1780 LYS Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1867 VAL Chi-restraints excluded: chain D residue 2014 GLU Chi-restraints excluded: chain D residue 2048 GLU Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2272 SER Chi-restraints excluded: chain D residue 2281 THR Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2400 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 503 optimal weight: 10.0000 chunk 675 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 584 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 634 optimal weight: 7.9990 chunk 265 optimal weight: 40.0000 chunk 651 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.109714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.071047 restraints weight = 1051418.172| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 6.68 r_work: 0.3256 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 66276 Z= 0.326 Angle : 0.573 13.935 89591 Z= 0.313 Chirality : 0.036 0.169 10297 Planarity : 0.003 0.042 11335 Dihedral : 5.184 88.952 8902 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.82 % Allowed : 18.69 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.09), residues: 7909 helix: 1.82 (0.07), residues: 5532 sheet: -0.30 (0.24), residues: 446 loop : -0.17 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2184 HIS 0.010 0.001 HIS B2558 PHE 0.017 0.002 PHE A1082 TYR 0.018 0.002 TYR C1107 ARG 0.010 0.001 ARG C 738 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34305.55 seconds wall clock time: 590 minutes 20.48 seconds (35420.48 seconds total)