Starting phenix.real_space_refine on Tue Mar 19 20:48:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3d_15825/03_2024/8b3d_15825_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3d_15825/03_2024/8b3d_15825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3d_15825/03_2024/8b3d_15825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3d_15825/03_2024/8b3d_15825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3d_15825/03_2024/8b3d_15825_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3d_15825/03_2024/8b3d_15825_trim_updated.pdb" } resolution = 2.6 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= 0.003 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: 10 Type Number sf(0) Gaussians Zn 10 6.06 5 P 104 5.49 5 Mg 2 5.21 5 S 286 5.16 5 Be 1 3.05 5 C 30545 2.51 5 N 8563 2.21 5 O 9340 1.98 5 F 3 1.80 5 H 46942 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A VAL 110": "CG1" <-> "CG2" "HG11" <-> "HG21" "HG12" <-> "HG22" "HG13" <-> "HG23" Residue "A ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A GLU 1085": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ARG 1206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1302": "OE1" <-> "OE2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A GLU 1333": "OE1" <-> "OE2" Residue "A GLU 1364": "OE1" <-> "OE2" Residue "A ARG 1375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "A GLU 1456": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 242": not complete - not flipped Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B LEU 393": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "B ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B ARG 638": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B GLU 1026": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "M GLU 21": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a GLU 238": "OE1" <-> "OE2" Residue "b ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 584": "OE1" <-> "OE2" Residue "b ARG 593": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 637": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 666": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 792": "OE1" <-> "OE2" Residue "b ARG 876": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 915": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 950": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 985": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c GLU 10": "OE1" <-> "OE2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c GLU 23": "OE1" <-> "OE2" Residue "c GLU 53": "OE1" <-> "OE2" Residue "c GLU 56": "OE1" <-> "OE2" Residue "c GLU 67": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 104": "OE1" <-> "OE2" Residue "c GLU 122": "OE1" <-> "OE2" Residue "c GLU 578": "OE1" <-> "OE2" Residue "d ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 54": "OE1" <-> "OE2" Residue "d GLU 72": "OE1" <-> "OE2" Residue "d ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 160": "OE1" <-> "OE2" Residue "d GLU 194": "OE1" <-> "OE2" Residue "d ARG 198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 201": "OE1" <-> "OE2" Residue "d GLU 235": "OE1" <-> "OE2" Residue "d GLU 277": "OE1" <-> "OE2" Residue "d GLU 303": "OE1" <-> "OE2" Residue "d GLU 351": "OE1" <-> "OE2" Residue "d ARG 369": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 728": "OE1" <-> "OE2" Residue "d GLU 741": "OE1" <-> "OE2" Residue "d GLU 800": "OE1" <-> "OE2" Residue "d GLU 840": "OE1" <-> "OE2" Residue "d GLU 842": "OE1" <-> "OE2" Residue "d GLU 863": "OE1" <-> "OE2" Residue "d GLU 865": "OE1" <-> "OE2" Residue "d GLU 875": "OE1" <-> "OE2" Residue "d GLU 896": "OE1" <-> "OE2" Residue "d ARG 900": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 989": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 1079": "OE1" <-> "OE2" Residue "d ARG 1080": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 1102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 1107": "OE1" <-> "OE2" Residue "d ARG 1138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 95796 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 22460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 22460 Classifications: {'peptide': 1409} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1339} Chain breaks: 4 Chain: "B" Number of atoms: 18131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1130, 18131 Classifications: {'peptide': 1130} Link IDs: {'PTRANS': 53, 'TRANS': 1076} Chain breaks: 3 Chain: "C" Number of atoms: 4120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 4120 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1985 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3457 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2665 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2333 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1827 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1086 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 781 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 968 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "N" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 913 Classifications: {'DNA': 40} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "P" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 330 Classifications: {'RNA': 10} Modifications used: {'3*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1078 Classifications: {'DNA': 52} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 51} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {' DC:plan2': 1, ' DG:plan': 2, ' DG:plan2': 2, ' DC:plan': 1, ' DT:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "a" Number of atoms: 5624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5624 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain: "b" Number of atoms: 8561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 8561 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 21, 'TRANS': 498} Chain breaks: 3 Chain: "c" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 3910 Classifications: {'peptide': 264} Modifications used: {'NH3': 1} Incomplete info: {'backbone_only': 11} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 248} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "d" Number of atoms: 12321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 12321 Classifications: {'peptide': 781} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 754} Chain breaks: 7 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 942 SG CYS A 71 72.322 51.208 107.940 1.00 22.32 S ATOM 983 SG CYS A 74 69.478 51.109 105.510 1.00 19.34 S ATOM 1070 SG CYS A 81 72.333 53.074 104.501 1.00 14.62 S ATOM 1553 SG CYS A 111 54.890 90.587 128.056 1.00 31.83 S ATOM 1603 SG CYS A 114 51.869 88.954 129.365 1.00 30.64 S ATOM 2263 SG CYS A 154 51.552 91.970 127.916 1.00 35.14 S ATOM 2301 SG CYS A 184 53.173 91.605 131.497 1.00 34.95 S ATOM 39710 SG CYS B1119 55.235 58.799 107.208 1.00 15.87 S ATOM 39753 SG CYS B1122 57.235 61.901 108.275 1.00 16.24 S ATOM 39978 SG CYS B1137 58.254 58.637 109.652 1.00 20.07 S ATOM 40019 SG CYS B1140 54.747 60.458 110.468 1.00 25.67 S ATOM 41972 SG CYS C 88 107.251 36.225 50.864 1.00 17.51 S ATOM 41996 SG CYS C 90 107.980 35.695 54.512 1.00 22.48 S ATOM 42056 SG CYS C 94 110.446 35.701 51.933 1.00 9.96 S ATOM 42095 SG CYS C 97 108.970 39.177 52.807 1.00 8.27 S ATOM 56625 SG CYS I 17 99.119 137.951 121.011 1.00 22.10 S ATOM 56667 SG CYS I 20 98.803 134.260 121.981 1.00 24.12 S ATOM 56987 SG CYS I 39 95.675 135.224 121.166 1.00 25.49 S ATOM 57035 SG CYS I 42 97.423 137.260 123.737 1.00 28.23 S ATOM 57708 SG CYS I 86 112.586 138.937 78.749 1.00 30.29 S ATOM 57757 SG CYS I 89 116.260 139.012 78.557 1.00 33.00 S ATOM 58149 SG CYS I 114 115.020 135.798 79.042 1.00 24.24 S ATOM 58214 SG CYS I 119 115.042 138.469 81.851 1.00 27.51 S ATOM 58436 SG CYS J 7 113.088 70.209 51.386 1.00 5.73 S ATOM 58480 SG CYS J 10 112.959 68.584 47.950 1.00 5.27 S ATOM 59005 SG CYS J 44 112.293 72.501 48.545 1.00 3.00 S ATOM 59015 SG CYS J 45 115.619 70.863 48.507 1.00 1.32 S ATOM 61379 SG CYS L 19 127.493 56.168 90.305 1.00 19.42 S ATOM 61411 SG CYS L 22 130.736 54.634 89.596 1.00 22.23 S ATOM 61641 SG CYS L 36 128.900 53.127 92.223 1.00 24.01 S ATOM 61690 SG CYS L 39 130.224 56.953 92.602 1.00 24.58 S ATOM 62152 SG CYS M 26 84.481 103.529 140.556 1.00 34.19 S ATOM 62196 SG CYS M 29 82.961 100.242 141.814 1.00 31.11 S ATOM 62514 SG CYS M 50 80.850 102.531 140.167 1.00 33.14 S ATOM 62554 SG CYS M 53 82.155 103.651 143.579 1.00 32.93 S ATOM 82157 SG CYS c 567 60.474 154.610 90.898 1.00 44.82 S ATOM 82315 SG CYS c 577 63.553 156.123 92.599 1.00 43.58 S ATOM 82458 SG CYS c 585 62.539 152.375 93.183 1.00 44.02 S Time building chain proxies: 31.80, per 1000 atoms: 0.33 Number of scatterers: 95796 At special positions: 0 Unit cell: (149.1, 174.3, 233.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 10 29.99 S 286 16.00 P 104 15.00 Mg 2 11.99 F 3 9.00 O 9340 8.00 N 8563 7.00 C 30545 6.00 Be 1 4.00 H 46942 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.33 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 50 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 29 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 26 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 53 " pdb=" ZN c1001 " pdb="ZN ZN c1001 " - pdb=" ND1 HIS c 588 " pdb="ZN ZN c1001 " - pdb=" SG CYS c 567 " pdb="ZN ZN c1001 " - pdb=" SG CYS c 577 " pdb="ZN ZN c1001 " - pdb=" SG CYS c 585 " Number of angles added : 54 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 65 sheets defined 30.2% alpha, 17.2% beta 44 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 39.87 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.773A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.663A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 275 through 295 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 4.047A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.656A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 662 through 683 removed outlier: 4.049A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 947 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1053 through 1056 No H-bonds generated for 'chain 'A' and resid 1053 through 1056' Processing helix chain 'A' and resid 1062 through 1078 Processing helix chain 'A' and resid 1087 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1190 through 1197 Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1281 through 1295 removed outlier: 3.998A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 4.058A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1387 Processing helix chain 'A' and resid 1395 through 1404 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'B' and resid 19 through 36 removed outlier: 4.078A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.543A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 425 removed outlier: 3.702A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.817A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 679 through 682 Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 730 removed outlier: 4.386A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 767 No H-bonds generated for 'chain 'B' and resid 764 through 767' Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 969 through 971 No H-bonds generated for 'chain 'B' and resid 969 through 971' Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.529A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1057 No H-bonds generated for 'chain 'B' and resid 1055 through 1057' Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1153 through 1165 removed outlier: 3.512A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.538A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 269 Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 71 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'H' and resid 129 through 131 No H-bonds generated for 'chain 'H' and resid 129 through 131' Processing helix chain 'I' and resid 64 through 67 Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.869A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.732A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 51 removed outlier: 4.041A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 67 through 81 Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 15 through 28 Processing helix chain 'b' and resid 501 through 506 removed outlier: 3.686A pdb=" N LYS b 506 " --> pdb=" O PHE b 502 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 524 Processing helix chain 'b' and resid 539 through 551 Processing helix chain 'b' and resid 575 through 588 removed outlier: 3.671A pdb=" N MET b 578 " --> pdb=" O THR b 575 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N HIS b 579 " --> pdb=" O THR b 576 " (cutoff:3.500A) Processing helix chain 'b' and resid 607 through 617 Processing helix chain 'b' and resid 625 through 630 Processing helix chain 'b' and resid 632 through 635 No H-bonds generated for 'chain 'b' and resid 632 through 635' Processing helix chain 'b' and resid 648 through 651 Processing helix chain 'b' and resid 657 through 664 removed outlier: 3.764A pdb=" N GLN b 664 " --> pdb=" O LEU b 660 " (cutoff:3.500A) Processing helix chain 'b' and resid 682 through 692 Processing helix chain 'b' and resid 700 through 713 removed outlier: 5.065A pdb=" N VAL b 709 " --> pdb=" O GLU b 705 " (cutoff:3.500A) Proline residue: b 710 - end of helix Processing helix chain 'b' and resid 721 through 738 Processing helix chain 'b' and resid 770 through 780 Processing helix chain 'b' and resid 783 through 789 Processing helix chain 'b' and resid 796 through 807 Processing helix chain 'b' and resid 835 through 837 No H-bonds generated for 'chain 'b' and resid 835 through 837' Processing helix chain 'b' and resid 839 through 853 Processing helix chain 'b' and resid 865 through 877 Processing helix chain 'b' and resid 891 through 903 removed outlier: 4.737A pdb=" N GLN b 895 " --> pdb=" O ALA b 892 " (cutoff:3.500A) Proline residue: b 896 - end of helix Processing helix chain 'b' and resid 938 through 947 Processing helix chain 'b' and resid 968 through 987 removed outlier: 3.930A pdb=" N VAL b 986 " --> pdb=" O LEU b 982 " (cutoff:3.500A) Processing helix chain 'b' and resid 1388 through 1398 Processing helix chain 'c' and resid 3 through 14 Processing helix chain 'c' and resid 22 through 33 Processing helix chain 'c' and resid 36 through 50 Processing helix chain 'c' and resid 55 through 71 Processing helix chain 'c' and resid 74 through 90 removed outlier: 4.008A pdb=" N ASN c 82 " --> pdb=" O LEU c 78 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLN c 84 " --> pdb=" O VAL c 80 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU c 85 " --> pdb=" O SER c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 97 No H-bonds generated for 'chain 'c' and resid 95 through 97' Processing helix chain 'c' and resid 103 through 124 Processing helix chain 'c' and resid 129 through 140 Processing helix chain 'c' and resid 603 through 618 Processing helix chain 'c' and resid 662 through 665 No H-bonds generated for 'chain 'c' and resid 662 through 665' Processing helix chain 'c' and resid 668 through 676 Processing helix chain 'c' and resid 679 through 698 Processing helix chain 'd' and resid 251 through 253 No H-bonds generated for 'chain 'd' and resid 251 through 253' Processing helix chain 'd' and resid 367 through 369 No H-bonds generated for 'chain 'd' and resid 367 through 369' Processing helix chain 'd' and resid 987 through 990 Processing helix chain 'd' and resid 1045 through 1061 Processing helix chain 'd' and resid 1070 through 1074 Processing helix chain 'd' and resid 1091 through 1098 removed outlier: 3.718A pdb=" N PHE d1097 " --> pdb=" O LEU d1093 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU d1098 " --> pdb=" O ILE d1094 " (cutoff:3.500A) Processing helix chain 'd' and resid 1102 through 1108 Processing helix chain 'd' and resid 1126 through 1139 removed outlier: 4.069A pdb=" N ILE d1139 " --> pdb=" O GLU d1135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.153A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 362 through 366 Processing sheet with id= C, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.157A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 389 through 393 Processing sheet with id= E, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= F, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= G, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id= H, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 3.602A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id= J, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.743A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= L, first strand: chain 'B' and resid 140 through 144 removed outlier: 4.114A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= N, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= O, first strand: chain 'B' and resid 206 through 208 Processing sheet with id= P, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= Q, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= R, first strand: chain 'B' and resid 602 through 605 removed outlier: 6.595A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.741A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.259A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 794 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR B 944 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 796 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY B 946 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= V, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id= W, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id= X, first strand: chain 'B' and resid 121 through 126 removed outlier: 6.178A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 182 through 185 removed outlier: 6.744A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 99 through 106 removed outlier: 6.059A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 113 through 116 Processing sheet with id= AB, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.310A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 147 through 150 removed outlier: 7.700A pdb=" N GLN E 210 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.648A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 142 through 147 removed outlier: 3.947A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 118 through 120 Processing sheet with id= AH, first strand: chain 'G' and resid 50 through 54 removed outlier: 3.656A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.705A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 25 through 29 Processing sheet with id= AK, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= AL, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AM, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AN, first strand: chain 'M' and resid 35 through 40 Processing sheet with id= AO, first strand: chain 'a' and resid 30 through 32 Processing sheet with id= AP, first strand: chain 'a' and resid 36 through 38 removed outlier: 6.238A pdb=" N TYR a 82 " --> pdb=" O ASP a 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.876A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA a 86 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'a' and resid 102 through 107 removed outlier: 6.865A pdb=" N SER a 118 " --> pdb=" O GLU a 103 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL a 105 " --> pdb=" O THR a 116 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR a 116 " --> pdb=" O VAL a 105 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TRP a 107 " --> pdb=" O MET a 114 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET a 114 " --> pdb=" O TRP a 107 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP a 128 " --> pdb=" O THR a 134 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR a 134 " --> pdb=" O ASP a 128 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'a' and resid 168 through 172 Processing sheet with id= AT, first strand: chain 'a' and resid 210 through 215 removed outlier: 3.858A pdb=" N ARG a 210 " --> pdb=" O SER a 206 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'a' and resid 268 through 273 removed outlier: 3.791A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'a' and resid 307 through 312 removed outlier: 6.569A pdb=" N THR a 320 " --> pdb=" O GLN a 326 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN a 326 " --> pdb=" O THR a 320 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'b' and resid 528 through 530 Processing sheet with id= AX, first strand: chain 'b' and resid 569 through 572 Processing sheet with id= AY, first strand: chain 'b' and resid 959 through 961 removed outlier: 6.750A pdb=" N VAL b 929 " --> pdb=" O TYR b 960 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR b 913 " --> pdb=" O MET b 885 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'd' and resid 1088 through 1090 removed outlier: 6.985A pdb=" N ASN d 4 " --> pdb=" O ILE d1089 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE d1037 " --> pdb=" O ALA d 9 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'd' and resid 17 through 21 removed outlier: 6.229A pdb=" N VAL d 43 " --> pdb=" O PRO d 51 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'd' and resid 61 through 67 removed outlier: 6.585A pdb=" N LEU d 80 " --> pdb=" O ALA d 62 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET d 64 " --> pdb=" O PHE d 78 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE d 78 " --> pdb=" O MET d 64 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU d 66 " --> pdb=" O LEU d 76 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU d 76 " --> pdb=" O LEU d 66 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU d 90 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR d 102 " --> pdb=" O GLU d 90 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS d 92 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE d 100 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER d 94 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'd' and resid 121 through 124 Processing sheet with id= BD, first strand: chain 'd' and resid 201 through 204 removed outlier: 6.426A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'd' and resid 218 through 221 Processing sheet with id= BF, first strand: chain 'd' and resid 258 through 263 removed outlier: 6.835A pdb=" N GLY d 274 " --> pdb=" O VAL d 259 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS d 261 " --> pdb=" O LEU d 272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU d 272 " --> pdb=" O HIS d 261 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG d 263 " --> pdb=" O ARG d 270 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG d 270 " --> pdb=" O ARG d 263 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N MET d 282 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU d 304 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU d 284 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL d 302 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU d 286 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU d 300 " --> pdb=" O GLU d 286 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'd' and resid 313 through 316 removed outlier: 6.025A pdb=" N LYS d 335 " --> pdb=" O ALA d 349 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA d 349 " --> pdb=" O LYS d 335 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'd' and resid 361 through 364 removed outlier: 4.036A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.491A pdb=" N LEU d 736 " --> pdb=" O ARG d 722 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE d 724 " --> pdb=" O GLY d 734 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY d 734 " --> pdb=" O ILE d 724 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR d 726 " --> pdb=" O CYS d 732 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS d 732 " --> pdb=" O TYR d 726 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP d 795 " --> pdb=" O VAL d 801 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL d 801 " --> pdb=" O ASP d 795 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'd' and resid 811 through 819 removed outlier: 6.681A pdb=" N GLY d 832 " --> pdb=" O LEU d 814 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU d 816 " --> pdb=" O ILE d 830 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE d 830 " --> pdb=" O LEU d 816 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER d 818 " --> pdb=" O TYR d 828 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR d 828 " --> pdb=" O SER d 818 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN d 852 " --> pdb=" O THR d 860 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR d 860 " --> pdb=" O GLN d 852 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER d 854 " --> pdb=" O LEU d 858 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU d 858 " --> pdb=" O SER d 854 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'd' and resid 873 through 876 removed outlier: 3.719A pdb=" N CYS d 903 " --> pdb=" O LEU d 890 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU d 892 " --> pdb=" O THR d 901 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR d 901 " --> pdb=" O GLU d 892 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 911 through 917 removed outlier: 6.585A pdb=" N GLY d 924 " --> pdb=" O LEU d 912 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU d 914 " --> pdb=" O LEU d 922 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU d 922 " --> pdb=" O LEU d 914 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR d 916 " --> pdb=" O PHE d 920 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE d 920 " --> pdb=" O THR d 916 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA d 934 " --> pdb=" O GLU d 944 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU d 944 " --> pdb=" O ALA d 934 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS d 936 " --> pdb=" O PHE d 942 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE d 942 " --> pdb=" O LYS d 936 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'd' and resid 954 through 959 removed outlier: 6.736A pdb=" N ALA d 968 " --> pdb=" O SER d 955 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL d 957 " --> pdb=" O LEU d 966 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU d 966 " --> pdb=" O VAL d 957 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE d 959 " --> pdb=" O ASN d 964 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN d 964 " --> pdb=" O ILE d 959 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN d 973 " --> pdb=" O GLU d 969 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN d 978 " --> pdb=" O GLU d 994 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU d 994 " --> pdb=" O GLN d 978 " (cutoff:3.500A) 1612 hydrogen bonds defined for protein. 4578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 43.62 Time building geometry restraints manager: 67.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 46851 1.02 - 1.22: 174 1.22 - 1.42: 20788 1.42 - 1.62: 28672 1.62 - 1.82: 446 Bond restraints: 96931 Sorted by residual: bond pdb=" CB MET G 1 " pdb=" CG MET G 1 " ideal model delta sigma weight residual 1.520 1.274 0.246 3.00e-02 1.11e+03 6.74e+01 bond pdb=" ND2 ASN a 33 " pdb="HD22 ASN a 33 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN a 33 " pdb="HD21 ASN a 33 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN d1049 " pdb="HD21 ASN d1049 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN d1049 " pdb="HD22 ASN d1049 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 96926 not shown) Histogram of bond angle deviations from ideal: 78.51 - 94.96: 142 94.96 - 111.41: 105651 111.41 - 127.86: 68137 127.86 - 144.32: 742 144.32 - 160.77: 14 Bond angle restraints: 174686 Sorted by residual: angle pdb=" CG ARG A1286 " pdb=" CD ARG A1286 " pdb=" NE ARG A1286 " ideal model delta sigma weight residual 112.00 160.77 -48.77 2.20e+00 2.07e-01 4.91e+02 angle pdb=" CG ARG A 958 " pdb=" CD ARG A 958 " pdb=" NE ARG A 958 " ideal model delta sigma weight residual 112.00 159.16 -47.16 2.20e+00 2.07e-01 4.59e+02 angle pdb=" CA GLN G 28 " pdb=" CB GLN G 28 " pdb=" CG GLN G 28 " ideal model delta sigma weight residual 114.10 150.98 -36.88 2.00e+00 2.50e-01 3.40e+02 angle pdb=" CA GLN A 711 " pdb=" CB GLN A 711 " pdb=" CG GLN A 711 " ideal model delta sigma weight residual 114.10 150.52 -36.42 2.00e+00 2.50e-01 3.32e+02 angle pdb=" CA LYS A 105 " pdb=" CB LYS A 105 " pdb=" CG LYS A 105 " ideal model delta sigma weight residual 114.10 148.80 -34.70 2.00e+00 2.50e-01 3.01e+02 ... (remaining 174681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 43873 35.99 - 71.98: 1407 71.98 - 107.98: 57 107.98 - 143.97: 2 143.97 - 179.96: 4 Dihedral angle restraints: 45343 sinusoidal: 25631 harmonic: 19712 Sorted by residual: dihedral pdb=" CD ARG B 242 " pdb=" NE ARG B 242 " pdb=" CZ ARG B 242 " pdb=" NH1 ARG B 242 " ideal model delta sinusoidal sigma weight residual 0.00 -179.96 179.96 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA GLU A1478 " pdb=" C GLU A1478 " pdb=" N LYS A1479 " pdb=" CA LYS A1479 " ideal model delta harmonic sigma weight residual 180.00 125.60 54.40 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ARG L 37 " pdb=" C ARG L 37 " pdb=" N GLU L 38 " pdb=" CA GLU L 38 " ideal model delta harmonic sigma weight residual 180.00 128.58 51.42 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 45340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.594: 7547 0.594 - 1.188: 10 1.188 - 1.782: 3 1.782 - 2.376: 4 2.376 - 2.970: 2 Chirality restraints: 7566 Sorted by residual: chirality pdb=" CB VAL A 110 " pdb=" CA VAL A 110 " pdb=" CG1 VAL A 110 " pdb=" CG2 VAL A 110 " both_signs ideal model delta sigma weight residual False -2.63 0.34 -2.97 2.00e-01 2.50e+01 2.21e+02 chirality pdb=" CG LEU B 393 " pdb=" CB LEU B 393 " pdb=" CD1 LEU B 393 " pdb=" CD2 LEU B 393 " both_signs ideal model delta sigma weight residual False -2.59 0.12 -2.71 2.00e-01 2.50e+01 1.83e+02 chirality pdb=" CB VAL B 301 " pdb=" CA VAL B 301 " pdb=" CG1 VAL B 301 " pdb=" CG2 VAL B 301 " both_signs ideal model delta sigma weight residual False -2.63 -0.51 -2.12 2.00e-01 2.50e+01 1.12e+02 ... (remaining 7563 not shown) Planarity restraints: 14088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 388 " 0.094 2.00e-02 2.50e+03 6.53e-02 1.28e+02 pdb=" CG TYR B 388 " -0.184 2.00e-02 2.50e+03 pdb=" CD1 TYR B 388 " 0.081 2.00e-02 2.50e+03 pdb=" CD2 TYR B 388 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 388 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR B 388 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 388 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR B 388 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR B 388 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR B 388 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR B 388 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR B 388 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 397 " 0.056 2.00e-02 2.50e+03 6.27e-02 1.18e+02 pdb=" CG PHE A 397 " -0.168 2.00e-02 2.50e+03 pdb=" CD1 PHE A 397 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 397 " 0.119 2.00e-02 2.50e+03 pdb=" CE1 PHE A 397 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 397 " -0.025 2.00e-02 2.50e+03 pdb=" CZ PHE A 397 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 397 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 397 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE A 397 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 397 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 397 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 112 " -0.056 2.00e-02 2.50e+03 6.15e-02 1.13e+02 pdb=" CG PHE A 112 " 0.164 2.00e-02 2.50e+03 pdb=" CD1 PHE A 112 " -0.118 2.00e-02 2.50e+03 pdb=" CD2 PHE A 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 112 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE A 112 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 112 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 112 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 PHE A 112 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 112 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 112 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 112 " 0.007 2.00e-02 2.50e+03 ... (remaining 14085 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 1723 2.05 - 2.69: 152369 2.69 - 3.33: 287719 3.33 - 3.96: 386958 3.96 - 4.60: 601202 Nonbonded interactions: 1429971 Sorted by model distance: nonbonded pdb=" OD2 ASP a 37 " pdb=" OH TYR a 81 " model vdw 1.418 2.200 nonbonded pdb="HD22 ASN a 33 " pdb=" HB3 ALA a 360 " model vdw 1.419 2.270 nonbonded pdb=" H ILE E 84 " pdb=" OP1 DG N 45 " model vdw 1.544 1.850 nonbonded pdb=" OD1 ASN B1120 " pdb=" HG SER B1147 " model vdw 1.566 1.850 nonbonded pdb=" O TYR A 413 " pdb=" HD1 HIS A 449 " model vdw 1.575 1.850 ... (remaining 1429966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.060 Extract box with map and model: 17.550 Check model and map are aligned: 1.040 Set scattering table: 0.670 Process input model: 303.530 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 340.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.010 0.246 49989 Z= 0.661 Angle : 1.661 48.770 67932 Z= 0.838 Chirality : 0.101 2.970 7566 Planarity : 0.009 0.177 8443 Dihedral : 16.227 179.962 19213 Min Nonbonded Distance : 1.418 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.08 % Allowed : 0.93 % Favored : 98.99 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.11), residues: 5802 helix: -0.23 (0.11), residues: 1893 sheet: -0.96 (0.15), residues: 1132 loop : -0.93 (0.11), residues: 2777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 548 HIS 0.057 0.003 HIS A1082 PHE 0.170 0.003 PHE A 397 TYR 0.186 0.003 TYR B 388 ARG 0.134 0.005 ARG C 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 1055 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1051 time to evaluate : 5.600 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: A 438 LEU cc_start: 0.8485 (mp) cc_final: 0.8278 (mp) REVERT: A 495 ASP cc_start: 0.7890 (p0) cc_final: 0.7560 (p0) REVERT: A 637 MET cc_start: 0.8550 (ptt) cc_final: 0.8345 (ptt) REVERT: A 818 GLU cc_start: 0.7311 (mp0) cc_final: 0.7053 (mp0) REVERT: A 1003 ASP cc_start: 0.6926 (p0) cc_final: 0.6707 (p0) REVERT: A 1086 MET cc_start: 0.8901 (mmm) cc_final: 0.8499 (mmm) REVERT: A 1221 MET cc_start: 0.7379 (mmm) cc_final: 0.7157 (mmm) REVERT: A 1434 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7218 (mt-10) REVERT: B 385 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7610 (ttm-80) REVERT: B 697 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8189 (mm-30) REVERT: B 840 MET cc_start: 0.6890 (mtp) cc_final: 0.6552 (mtp) REVERT: B 1172 MET cc_start: 0.8223 (mmm) cc_final: 0.7979 (mmm) REVERT: E 59 THR cc_start: 0.7390 (t) cc_final: 0.7085 (m) REVERT: E 94 MET cc_start: 0.6276 (ttm) cc_final: 0.6067 (ttm) REVERT: E 147 GLU cc_start: 0.7512 (tt0) cc_final: 0.7213 (tp30) REVERT: J 57 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7842 (mm-30) REVERT: a 22 GLU cc_start: 0.7751 (tp30) cc_final: 0.7393 (mm-30) REVERT: c 38 GLN cc_start: 0.0515 (tt0) cc_final: 0.0164 (tm130) REVERT: c 691 ARG cc_start: 0.5450 (ttt180) cc_final: 0.5224 (ttm-80) REVERT: d 954 MET cc_start: 0.8630 (mmm) cc_final: 0.8388 (mmm) outliers start: 4 outliers final: 0 residues processed: 1053 average time/residue: 3.0281 time to fit residues: 4000.8598 Evaluate side-chains 860 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 860 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 498 optimal weight: 20.0000 chunk 447 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 301 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 chunk 462 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 344 optimal weight: 0.6980 chunk 535 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 288 ASN A 757 GLN A 926 ASN A1078 GLN B 486 ASN B 593 GLN B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 145 GLN C 260 GLN D 128 GLN E 95 GLN E 129 GLN E 174 GLN G 24 ASN I 45 GLN M 30 ASN ** a 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN a 241 ASN a 326 GLN c 52 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 111 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN d 797 HIS d 964 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 49989 Z= 0.229 Angle : 0.656 14.146 67932 Z= 0.344 Chirality : 0.052 1.804 7566 Planarity : 0.007 0.208 8443 Dihedral : 13.926 179.258 7557 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.02 % Favored : 95.97 % Rotamer: Outliers : 2.17 % Allowed : 9.65 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.11), residues: 5802 helix: 0.40 (0.12), residues: 1867 sheet: -0.87 (0.15), residues: 1149 loop : -0.72 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.007 0.001 HIS B 387 PHE 0.039 0.002 PHE A 112 TYR 0.042 0.002 TYR B 388 ARG 0.017 0.001 ARG A1286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 1034 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 922 time to evaluate : 5.648 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: A 231 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6649 (mm-30) REVERT: A 861 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7251 (mm-40) REVERT: A 1003 ASP cc_start: 0.6970 (p0) cc_final: 0.6764 (p0) REVERT: A 1451 MET cc_start: 0.8613 (mmm) cc_final: 0.8405 (mmm) REVERT: B 298 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7696 (mmm) REVERT: B 1163 MET cc_start: 0.8083 (mtt) cc_final: 0.7827 (mtt) REVERT: B 1172 MET cc_start: 0.8289 (mmm) cc_final: 0.8001 (mmm) REVERT: E 147 GLU cc_start: 0.7371 (tt0) cc_final: 0.7042 (tp30) REVERT: J 57 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7805 (mm-30) REVERT: L 16 ILE cc_start: 0.7817 (tt) cc_final: 0.7615 (pp) REVERT: a 22 GLU cc_start: 0.7728 (tp30) cc_final: 0.7501 (mm-30) REVERT: c 38 GLN cc_start: 0.0583 (tt0) cc_final: 0.0143 (tm130) REVERT: c 71 ARG cc_start: 0.2324 (tmt170) cc_final: 0.2117 (tmt-80) REVERT: d 954 MET cc_start: 0.8689 (mmm) cc_final: 0.8400 (mmm) outliers start: 112 outliers final: 33 residues processed: 964 average time/residue: 3.0266 time to fit residues: 3650.0789 Evaluate side-chains 891 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 855 time to evaluate : 5.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain b residue 584 GLU Chi-restraints excluded: chain c residue 111 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 297 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 445 optimal weight: 0.9990 chunk 364 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 536 optimal weight: 3.9990 chunk 579 optimal weight: 9.9990 chunk 478 optimal weight: 5.9990 chunk 532 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 430 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 757 GLN A1077 ASN A1078 GLN A1332 GLN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN a 187 GLN a 241 ASN ** b 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 GLN d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 49989 Z= 0.341 Angle : 0.626 11.625 67932 Z= 0.329 Chirality : 0.051 1.601 7566 Planarity : 0.005 0.071 8443 Dihedral : 13.780 179.146 7557 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.92 % Allowed : 11.50 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 5802 helix: 0.71 (0.12), residues: 1881 sheet: -0.66 (0.15), residues: 1153 loop : -0.66 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 203 HIS 0.007 0.001 HIS B 939 PHE 0.027 0.002 PHE A 112 TYR 0.024 0.002 TYR B1048 ARG 0.012 0.001 ARG B 613 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 1016 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 917 time to evaluate : 5.810 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: A 493 ASN cc_start: 0.8324 (t0) cc_final: 0.8100 (t0) REVERT: A 1350 LYS cc_start: 0.7449 (ttmt) cc_final: 0.7162 (ttmt) REVERT: A 1451 MET cc_start: 0.8598 (mmm) cc_final: 0.8394 (mmm) REVERT: B 302 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8030 (mttt) REVERT: B 668 LEU cc_start: 0.9065 (tp) cc_final: 0.8843 (tp) REVERT: B 733 MET cc_start: 0.8150 (mtt) cc_final: 0.7874 (mtt) REVERT: B 894 THR cc_start: 0.8095 (m) cc_final: 0.7795 (m) REVERT: B 1172 MET cc_start: 0.8370 (mmm) cc_final: 0.8030 (mmm) REVERT: C 228 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6818 (ttp80) REVERT: C 268 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6117 (tp40) REVERT: E 110 MET cc_start: 0.7570 (ttm) cc_final: 0.7361 (ttt) REVERT: E 147 GLU cc_start: 0.7422 (tt0) cc_final: 0.7069 (tp30) REVERT: H 136 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7005 (mp0) REVERT: J 1 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7192 (mtp) REVERT: J 55 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8246 (tt) REVERT: J 57 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7800 (mm-30) REVERT: K 32 LEU cc_start: 0.9200 (mm) cc_final: 0.8920 (mp) REVERT: K 97 GLU cc_start: 0.7528 (tt0) cc_final: 0.7266 (tt0) REVERT: a 22 GLU cc_start: 0.7745 (tp30) cc_final: 0.7538 (mm-30) REVERT: b 752 MET cc_start: 0.5559 (pmm) cc_final: 0.4920 (pmm) REVERT: c 38 GLN cc_start: 0.0690 (tt0) cc_final: 0.0207 (tm130) REVERT: c 691 ARG cc_start: 0.6855 (mpp-170) cc_final: 0.6635 (ttm-80) REVERT: d 954 MET cc_start: 0.8831 (mmm) cc_final: 0.8507 (mmm) outliers start: 99 outliers final: 49 residues processed: 968 average time/residue: 3.0331 time to fit residues: 3667.5937 Evaluate side-chains 916 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 863 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain b residue 584 GLU Chi-restraints excluded: chain b residue 634 ASP Chi-restraints excluded: chain b residue 846 SER Chi-restraints excluded: chain b residue 858 VAL Chi-restraints excluded: chain c residue 107 GLN Chi-restraints excluded: chain c residue 694 GLN Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 1071 SER Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 530 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 360 optimal weight: 3.9990 chunk 538 optimal weight: 0.8980 chunk 570 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 510 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN B 312 GLN B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN E 43 GLN E 107 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN a 241 ASN a 326 GLN b 992 GLN d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 49989 Z= 0.268 Angle : 0.577 11.507 67932 Z= 0.301 Chirality : 0.049 1.535 7566 Planarity : 0.004 0.077 8443 Dihedral : 13.655 179.862 7557 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.67 % Allowed : 13.13 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 5802 helix: 0.89 (0.12), residues: 1891 sheet: -0.57 (0.15), residues: 1150 loop : -0.58 (0.12), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 203 HIS 0.006 0.001 HIS B 699 PHE 0.016 0.002 PHE d1030 TYR 0.017 0.001 TYR B1048 ARG 0.008 0.001 ARG A 749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 972 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 886 time to evaluate : 5.724 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: A 105 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7940 (ttpt) REVERT: A 493 ASN cc_start: 0.8358 (t0) cc_final: 0.8150 (t0) REVERT: A 1228 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6254 (mmm) REVERT: A 1350 LYS cc_start: 0.7495 (ttmt) cc_final: 0.7182 (ttmt) REVERT: A 1478 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6668 (tm-30) REVERT: B 554 GLU cc_start: 0.6614 (pm20) cc_final: 0.6414 (pm20) REVERT: B 830 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: B 891 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7266 (t0) REVERT: B 1172 MET cc_start: 0.8399 (mmm) cc_final: 0.8074 (mmm) REVERT: C 260 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7392 (tp-100) REVERT: C 268 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.6125 (tp40) REVERT: E 70 ASP cc_start: 0.7350 (t70) cc_final: 0.6974 (t0) REVERT: E 147 GLU cc_start: 0.7406 (tt0) cc_final: 0.7034 (tp30) REVERT: H 136 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7037 (mp0) REVERT: J 1 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7145 (mtp) REVERT: K 32 LEU cc_start: 0.9180 (mm) cc_final: 0.8908 (mp) REVERT: a 12 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8361 (mm) REVERT: a 22 GLU cc_start: 0.7734 (tp30) cc_final: 0.7519 (mm-30) REVERT: b 616 HIS cc_start: 0.5627 (t-90) cc_final: 0.5407 (t-90) REVERT: b 752 MET cc_start: 0.5597 (pmm) cc_final: 0.4980 (pmm) REVERT: b 761 GLU cc_start: 0.5667 (pp20) cc_final: 0.5240 (pp20) REVERT: b 796 PHE cc_start: 0.7421 (m-80) cc_final: 0.7203 (m-80) REVERT: c 38 GLN cc_start: 0.0818 (tt0) cc_final: 0.0312 (tm130) REVERT: c 691 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6492 (mtp180) REVERT: d 954 MET cc_start: 0.8773 (mmm) cc_final: 0.8483 (mmm) outliers start: 86 outliers final: 45 residues processed: 927 average time/residue: 3.0316 time to fit residues: 3513.6999 Evaluate side-chains 910 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 856 time to evaluate : 5.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain b residue 584 GLU Chi-restraints excluded: chain b residue 846 SER Chi-restraints excluded: chain b residue 858 VAL Chi-restraints excluded: chain c residue 11 GLU Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 691 ARG Chi-restraints excluded: chain c residue 694 GLN Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 474 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 424 optimal weight: 3.9990 chunk 235 optimal weight: 0.3980 chunk 486 optimal weight: 30.0000 chunk 394 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 511 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 861 GLN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 344 GLN B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS B1068 GLN E 98 ASN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 ASN a 79 GLN a 187 GLN a 241 ASN a 289 ASN b 992 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN d 261 HIS ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.143 49989 Z= 0.494 Angle : 0.656 11.633 67932 Z= 0.345 Chirality : 0.053 1.569 7566 Planarity : 0.005 0.091 8443 Dihedral : 13.803 179.975 7557 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.35 % Allowed : 13.50 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 5802 helix: 0.68 (0.12), residues: 1892 sheet: -0.60 (0.15), residues: 1174 loop : -0.60 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 203 HIS 0.009 0.001 HIS B 699 PHE 0.024 0.002 PHE A 592 TYR 0.028 0.002 TYR B 160 ARG 0.009 0.001 ARG B 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 1009 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 888 time to evaluate : 5.792 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: A 105 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8093 (ttpt) REVERT: A 493 ASN cc_start: 0.8425 (t0) cc_final: 0.8211 (t0) REVERT: A 500 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7786 (mt-10) REVERT: A 954 ARG cc_start: 0.7619 (ptt90) cc_final: 0.7419 (ptp90) REVERT: A 1011 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7183 (mm-30) REVERT: A 1344 MET cc_start: 0.7025 (tpt) cc_final: 0.6448 (tpt) REVERT: A 1350 LYS cc_start: 0.7569 (ttmt) cc_final: 0.7272 (ttmt) REVERT: A 1472 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: B 224 CYS cc_start: 0.7917 (t) cc_final: 0.7632 (t) REVERT: B 302 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8031 (mttt) REVERT: B 554 GLU cc_start: 0.6951 (pm20) cc_final: 0.6731 (pt0) REVERT: B 591 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8159 (ttm170) REVERT: B 771 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: B 891 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7206 (t0) REVERT: B 1172 MET cc_start: 0.8377 (mmm) cc_final: 0.8118 (mmm) REVERT: C 228 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6912 (ttp80) REVERT: C 260 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7702 (tp-100) REVERT: E 137 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8701 (pt) REVERT: E 147 GLU cc_start: 0.7485 (tt0) cc_final: 0.7090 (tp30) REVERT: J 1 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7250 (mtp) REVERT: K 32 LEU cc_start: 0.9201 (mm) cc_final: 0.8916 (mp) REVERT: M 39 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.5342 (tpt) REVERT: a 22 GLU cc_start: 0.7764 (tp30) cc_final: 0.7559 (mm-30) REVERT: b 752 MET cc_start: 0.5779 (pmm) cc_final: 0.5241 (pmm) REVERT: b 796 PHE cc_start: 0.7543 (m-80) cc_final: 0.7336 (m-80) REVERT: b 858 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7906 (p) REVERT: c 38 GLN cc_start: 0.0907 (tt0) cc_final: 0.0368 (tm130) REVERT: d 954 MET cc_start: 0.8901 (mmm) cc_final: 0.8587 (mmm) REVERT: d 1002 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7382 (mm-30) outliers start: 121 outliers final: 65 residues processed: 953 average time/residue: 3.0850 time to fit residues: 3721.5204 Evaluate side-chains 937 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 858 time to evaluate : 5.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 357 CYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain a residue 114 MET Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 223 LEU Chi-restraints excluded: chain a residue 288 CYS Chi-restraints excluded: chain a residue 289 ASN Chi-restraints excluded: chain b residue 584 GLU Chi-restraints excluded: chain b residue 846 SER Chi-restraints excluded: chain b residue 858 VAL Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 107 GLN Chi-restraints excluded: chain d residue 207 TRP Chi-restraints excluded: chain d residue 1002 GLU Chi-restraints excluded: chain d residue 1071 SER Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 191 optimal weight: 1.9990 chunk 513 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 570 optimal weight: 3.9990 chunk 473 optimal weight: 3.9990 chunk 264 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 861 GLN A1310 HIS B 312 GLN B 344 GLN B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN a 79 GLN a 187 GLN a 241 ASN a 326 GLN ** b 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 992 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 49989 Z= 0.288 Angle : 0.588 11.469 67932 Z= 0.308 Chirality : 0.049 1.523 7566 Planarity : 0.004 0.067 8443 Dihedral : 13.683 179.773 7557 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.61 % Allowed : 14.89 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5802 helix: 0.85 (0.12), residues: 1892 sheet: -0.52 (0.15), residues: 1144 loop : -0.53 (0.12), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 203 HIS 0.006 0.001 HIS B 699 PHE 0.018 0.002 PHE C 229 TYR 0.020 0.001 TYR B 160 ARG 0.008 0.001 ARG A1345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 973 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 890 time to evaluate : 5.820 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: A 105 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8124 (ttpt) REVERT: A 493 ASN cc_start: 0.8375 (t0) cc_final: 0.8152 (t0) REVERT: A 1350 LYS cc_start: 0.7541 (ttmt) cc_final: 0.7235 (ttmt) REVERT: A 1472 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: B 206 TYR cc_start: 0.8206 (m-80) cc_final: 0.7573 (m-10) REVERT: B 224 CYS cc_start: 0.7867 (t) cc_final: 0.7594 (t) REVERT: B 302 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7949 (mttt) REVERT: B 771 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: B 891 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7247 (t0) REVERT: B 1172 MET cc_start: 0.8372 (mmm) cc_final: 0.8141 (mmm) REVERT: C 111 GLN cc_start: 0.7376 (pm20) cc_final: 0.7139 (pm20) REVERT: C 260 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7508 (tp-100) REVERT: E 147 GLU cc_start: 0.7395 (tt0) cc_final: 0.7022 (tp30) REVERT: F 50 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.6035 (pttt) REVERT: G 131 MET cc_start: 0.2017 (pmm) cc_final: 0.1709 (pmm) REVERT: J 1 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7199 (mtp) REVERT: K 32 LEU cc_start: 0.9176 (mm) cc_final: 0.8895 (mp) REVERT: L 38 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: M 39 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.5315 (tpt) REVERT: a 22 GLU cc_start: 0.7722 (tp30) cc_final: 0.7522 (mm-30) REVERT: b 752 MET cc_start: 0.5783 (pmm) cc_final: 0.5274 (pmm) REVERT: b 796 PHE cc_start: 0.7396 (m-80) cc_final: 0.7185 (m-80) REVERT: b 858 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7890 (p) REVERT: c 38 GLN cc_start: 0.0856 (tt0) cc_final: 0.0395 (tm130) REVERT: d 954 MET cc_start: 0.8873 (mmm) cc_final: 0.8597 (mmm) outliers start: 83 outliers final: 48 residues processed: 932 average time/residue: 3.0172 time to fit residues: 3518.6025 Evaluate side-chains 919 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 860 time to evaluate : 5.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 223 LEU Chi-restraints excluded: chain b residue 584 GLU Chi-restraints excluded: chain b residue 760 ASN Chi-restraints excluded: chain b residue 846 SER Chi-restraints excluded: chain b residue 858 VAL Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 107 GLN Chi-restraints excluded: chain d residue 207 TRP Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 550 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 325 optimal weight: 0.9990 chunk 416 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 480 optimal weight: 0.4980 chunk 318 optimal weight: 0.8980 chunk 568 optimal weight: 4.9990 chunk 355 optimal weight: 6.9990 chunk 346 optimal weight: 0.0770 chunk 262 optimal weight: 0.0470 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN A1310 HIS A1417 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN G 24 ASN a 79 GLN a 187 GLN a 241 ASN a 326 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 49989 Z= 0.163 Angle : 0.536 11.428 67932 Z= 0.279 Chirality : 0.048 1.488 7566 Planarity : 0.004 0.062 8443 Dihedral : 13.473 179.743 7557 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.28 % Allowed : 15.65 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5802 helix: 1.18 (0.12), residues: 1890 sheet: -0.48 (0.15), residues: 1141 loop : -0.39 (0.12), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.003 0.001 HIS B 699 PHE 0.027 0.001 PHE A 112 TYR 0.012 0.001 TYR B 160 ARG 0.009 0.000 ARG b 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 964 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 898 time to evaluate : 5.801 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: A 493 ASN cc_start: 0.8360 (t0) cc_final: 0.8139 (t0) REVERT: A 495 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 1472 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: B 206 TYR cc_start: 0.8110 (m-80) cc_final: 0.7641 (m-10) REVERT: B 224 CYS cc_start: 0.7851 (t) cc_final: 0.7574 (t) REVERT: B 891 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7213 (t0) REVERT: B 1172 MET cc_start: 0.8397 (mmm) cc_final: 0.8180 (mmm) REVERT: E 147 GLU cc_start: 0.7422 (tt0) cc_final: 0.7088 (tp30) REVERT: G 131 MET cc_start: 0.1868 (pmm) cc_final: 0.1585 (pmm) REVERT: K 32 LEU cc_start: 0.9147 (mm) cc_final: 0.8880 (mp) REVERT: L 38 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: M 39 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.5247 (tpt) REVERT: b 752 MET cc_start: 0.5712 (pmm) cc_final: 0.5252 (pmm) REVERT: b 761 GLU cc_start: 0.5695 (pp20) cc_final: 0.5257 (pp20) REVERT: c 38 GLN cc_start: 0.0758 (tt0) cc_final: 0.0351 (tm130) REVERT: d 954 MET cc_start: 0.8744 (mmm) cc_final: 0.8526 (mmm) outliers start: 66 outliers final: 32 residues processed: 928 average time/residue: 3.0344 time to fit residues: 3534.9881 Evaluate side-chains 897 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 860 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 548 TRP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 223 LEU Chi-restraints excluded: chain a residue 289 ASN Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 107 GLN Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 351 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 339 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 361 optimal weight: 0.9990 chunk 387 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 446 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN A 757 GLN A 861 GLN A1078 GLN A1310 HIS B 500 GLN B 518 HIS B 582 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN a 79 GLN a 187 GLN a 241 ASN a 326 GLN ** b 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 845 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 49989 Z= 0.289 Angle : 0.565 11.439 67932 Z= 0.295 Chirality : 0.049 1.505 7566 Planarity : 0.004 0.135 8443 Dihedral : 13.515 179.516 7557 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.50 % Allowed : 15.77 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 5802 helix: 1.13 (0.12), residues: 1897 sheet: -0.44 (0.15), residues: 1149 loop : -0.40 (0.12), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 203 HIS 0.005 0.001 HIS B 939 PHE 0.017 0.002 PHE A 592 TYR 0.019 0.001 TYR B 160 ARG 0.018 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 944 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 867 time to evaluate : 5.610 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: A 105 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8145 (ttpt) REVERT: A 493 ASN cc_start: 0.8350 (t0) cc_final: 0.8114 (t0) REVERT: A 495 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7805 (p0) REVERT: A 757 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7392 (mt0) REVERT: A 1472 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: B 206 TYR cc_start: 0.8161 (m-80) cc_final: 0.7583 (m-10) REVERT: B 224 CYS cc_start: 0.7865 (t) cc_final: 0.7574 (t) REVERT: B 302 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8049 (mttt) REVERT: B 891 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7179 (t0) REVERT: B 1172 MET cc_start: 0.8385 (mmm) cc_final: 0.8174 (mmm) REVERT: C 260 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7478 (tp-100) REVERT: E 147 GLU cc_start: 0.7373 (tt0) cc_final: 0.7026 (tp30) REVERT: K 32 LEU cc_start: 0.9161 (mm) cc_final: 0.8898 (mp) REVERT: L 38 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: M 39 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5284 (tpt) REVERT: b 752 MET cc_start: 0.5778 (pmm) cc_final: 0.5302 (pmm) REVERT: c 38 GLN cc_start: 0.0716 (tt0) cc_final: 0.0332 (tm130) REVERT: d 954 MET cc_start: 0.8852 (mmm) cc_final: 0.8584 (mmm) outliers start: 77 outliers final: 42 residues processed: 907 average time/residue: 3.0418 time to fit residues: 3462.2959 Evaluate side-chains 906 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 855 time to evaluate : 5.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 289 ASN Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 760 ASN Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 107 GLN Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 517 optimal weight: 3.9990 chunk 544 optimal weight: 4.9990 chunk 497 optimal weight: 30.0000 chunk 529 optimal weight: 0.8980 chunk 318 optimal weight: 0.5980 chunk 230 optimal weight: 0.7980 chunk 416 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 478 optimal weight: 2.9990 chunk 501 optimal weight: 8.9990 chunk 528 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN A 861 GLN A1078 GLN A1310 HIS B 500 GLN B 518 HIS B 650 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN ** a 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 GLN a 187 GLN a 326 GLN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 49989 Z= 0.335 Angle : 0.587 11.333 67932 Z= 0.306 Chirality : 0.049 1.513 7566 Planarity : 0.005 0.071 8443 Dihedral : 13.553 179.366 7557 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.24 % Allowed : 16.00 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 5802 helix: 1.06 (0.12), residues: 1900 sheet: -0.47 (0.15), residues: 1156 loop : -0.42 (0.12), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 203 HIS 0.006 0.001 HIS B 699 PHE 0.019 0.002 PHE A 592 TYR 0.022 0.002 TYR B 160 ARG 0.016 0.001 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 932 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 868 time to evaluate : 5.641 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: A 105 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8190 (ttpt) REVERT: A 493 ASN cc_start: 0.8339 (t0) cc_final: 0.8104 (t0) REVERT: A 495 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7822 (p0) REVERT: A 1472 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: B 224 CYS cc_start: 0.7899 (t) cc_final: 0.7601 (t) REVERT: B 891 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7183 (t0) REVERT: B 1172 MET cc_start: 0.8361 (mmm) cc_final: 0.8141 (mmm) REVERT: C 260 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7510 (tp-100) REVERT: E 147 GLU cc_start: 0.7382 (tt0) cc_final: 0.7027 (tp30) REVERT: J 1 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7107 (mtp) REVERT: K 32 LEU cc_start: 0.9166 (mm) cc_final: 0.8905 (mp) REVERT: M 39 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5293 (tpt) REVERT: c 38 GLN cc_start: 0.0732 (tt0) cc_final: 0.0335 (tm130) REVERT: d 954 MET cc_start: 0.8867 (mmm) cc_final: 0.8600 (mmm) outliers start: 64 outliers final: 43 residues processed: 904 average time/residue: 3.0185 time to fit residues: 3415.5849 Evaluate side-chains 909 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 859 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain a residue 289 ASN Chi-restraints excluded: chain b residue 760 ASN Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 107 GLN Chi-restraints excluded: chain d residue 207 TRP Chi-restraints excluded: chain d residue 1047 TRP Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 347 optimal weight: 1.9990 chunk 560 optimal weight: 4.9990 chunk 342 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 389 optimal weight: 10.0000 chunk 587 optimal weight: 8.9990 chunk 540 optimal weight: 3.9990 chunk 468 optimal weight: 0.0870 chunk 48 optimal weight: 0.3980 chunk 361 optimal weight: 0.4980 chunk 287 optimal weight: 30.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN A 861 GLN A1078 GLN A1291 ASN A1310 HIS B 460 HIS B 500 GLN B 518 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN M 58 GLN ** a 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 GLN a 187 GLN a 241 ASN a 326 GLN ** b 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 845 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 49989 Z= 0.193 Angle : 0.547 11.319 67932 Z= 0.284 Chirality : 0.048 1.488 7566 Planarity : 0.004 0.068 8443 Dihedral : 13.446 179.376 7557 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.05 % Allowed : 16.37 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5802 helix: 1.23 (0.12), residues: 1896 sheet: -0.43 (0.15), residues: 1131 loop : -0.34 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 203 HIS 0.005 0.001 HIS B 699 PHE 0.017 0.001 PHE A 766 TYR 0.015 0.001 TYR I 25 ARG 0.012 0.000 ARG B1150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11604 Ramachandran restraints generated. 5802 Oldfield, 0 Emsley, 5802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 549 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LYS 616 is missing expected H atoms. Skipping. Residue SER 657 is missing expected H atoms. Skipping. Residue LEU 658 is missing expected H atoms. Skipping. Residue THR 659 is missing expected H atoms. Skipping. Residue LEU 661 is missing expected H atoms. Skipping. Residue LYS 662 is missing expected H atoms. Skipping. Residue ALA 663 is missing expected H atoms. Skipping. Residue ALA 665 is missing expected H atoms. Skipping. Evaluate side-chains 928 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 874 time to evaluate : 6.784 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: A 493 ASN cc_start: 0.8370 (t0) cc_final: 0.8147 (t0) REVERT: A 495 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7756 (p0) REVERT: A 1472 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: B 206 TYR cc_start: 0.8122 (m-80) cc_final: 0.7525 (m-10) REVERT: B 224 CYS cc_start: 0.7842 (t) cc_final: 0.7556 (t) REVERT: B 891 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7151 (t0) REVERT: C 260 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7432 (tp-100) REVERT: E 147 GLU cc_start: 0.7395 (tt0) cc_final: 0.7048 (tp30) REVERT: K 32 LEU cc_start: 0.9122 (mm) cc_final: 0.8888 (mp) REVERT: M 39 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.5211 (tpt) REVERT: c 38 GLN cc_start: 0.0782 (tt0) cc_final: 0.0379 (tm130) REVERT: d 954 MET cc_start: 0.8827 (mmm) cc_final: 0.8598 (mmm) outliers start: 54 outliers final: 36 residues processed: 899 average time/residue: 3.1638 time to fit residues: 3602.8613 Evaluate side-chains 898 residues out of total 5200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 857 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 1290 SER Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 193 SER Chi-restraints excluded: chain a residue 206 SER Chi-restraints excluded: chain b residue 760 ASN Chi-restraints excluded: chain c residue 78 LEU Chi-restraints excluded: chain c residue 107 GLN Chi-restraints excluded: chain d residue 207 TRP Chi-restraints excluded: chain d residue 1047 TRP Chi-restraints excluded: chain d residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 371 optimal weight: 0.9980 chunk 498 optimal weight: 30.0000 chunk 143 optimal weight: 0.6980 chunk 431 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 468 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 481 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN A 757 GLN A 861 GLN A1078 GLN A1291 ASN A1310 HIS B 500 GLN B 518 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 79 GLN a 187 GLN a 241 ASN a 326 GLN ** b 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 GLN ** d 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.199822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127490 restraints weight = 141292.640| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.21 r_work: 0.3144 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 49989 Z= 0.214 Angle : 0.621 59.169 67932 Z= 0.338 Chirality : 0.048 1.489 7566 Planarity : 0.004 0.066 8443 Dihedral : 13.443 179.383 7557 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.93 % Allowed : 16.66 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 5802 helix: 1.24 (0.12), residues: 1895 sheet: -0.43 (0.15), residues: 1133 loop : -0.34 (0.12), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 203 HIS 0.005 0.001 HIS B 699 PHE 0.015 0.001 PHE d1030 TYR 0.014 0.001 TYR B 160 ARG 0.008 0.000 ARG A 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46659.90 seconds wall clock time: 799 minutes 2.61 seconds (47942.61 seconds total)