Starting phenix.real_space_refine on Tue Mar 19 05:48:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3f_15826/03_2024/8b3f_15826.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3f_15826/03_2024/8b3f_15826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3f_15826/03_2024/8b3f_15826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3f_15826/03_2024/8b3f_15826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3f_15826/03_2024/8b3f_15826.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3f_15826/03_2024/8b3f_15826.pdb" } resolution = 3.1 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: 8 Type Number sf(0) Gaussians Zn 9 6.06 5 P 102 5.49 5 Mg 1 5.21 5 S 277 5.16 5 C 29355 2.51 5 N 8183 2.21 5 O 8990 1.98 5 H 45119 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 GLU 492": "OE1" <-> "OE2" Residue "b ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 564": "OE1" <-> "OE2" 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 ARG 767": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 876": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 903": "OE1" <-> "OE2" Residue "b ARG 915": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 946": "OE1" <-> "OE2" Residue "b ARG 950": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 969": "OE1" <-> "OE2" Residue "b ARG 985": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 993": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 1003": "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: 92036 Number of models: 1 Model: "" Number of chains: 26 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} Modifications used: {'NH1NOTPRO': 1} 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: 8744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8744 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 21, 'TRANS': 512} Chain breaks: 3 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 942 SG CYS A 71 109.203 80.720 79.655 1.00 22.32 S ATOM 983 SG CYS A 74 108.701 77.204 78.476 1.00 19.34 S ATOM 1070 SG CYS A 81 105.792 79.335 78.331 1.00 14.62 S ATOM 1553 SG CYS A 111 95.755 68.806 123.660 1.00 31.83 S ATOM 1603 SG CYS A 114 98.632 66.603 124.276 1.00 30.64 S ATOM 2263 SG CYS A 154 95.584 65.549 125.221 1.00 35.14 S ATOM 2301 SG CYS A 184 97.458 68.384 127.230 1.00 34.95 S ATOM 39710 SG CYS B1119 107.927 64.004 87.966 1.00 15.87 S ATOM 39753 SG CYS B1122 105.593 66.009 90.267 1.00 16.24 S ATOM 39978 SG CYS B1137 108.586 67.708 88.946 1.00 20.07 S ATOM 40019 SG CYS B1140 108.680 64.608 91.528 1.00 25.67 S ATOM 41972 SG CYS C 88 77.638 93.552 20.147 1.00 17.51 S ATOM 41996 SG CYS C 90 79.935 95.596 22.307 1.00 22.48 S ATOM 42056 SG CYS C 94 77.730 96.947 19.848 1.00 9.96 S ATOM 42095 SG CYS C 97 76.005 95.626 23.058 1.00 8.27 S ATOM 56625 SG CYS I 17 42.700 103.640 138.521 1.00 22.10 S ATOM 56667 SG CYS I 20 46.171 103.985 136.941 1.00 24.12 S ATOM 56987 SG CYS I 39 45.870 100.710 137.691 1.00 25.49 S ATOM 57035 SG CYS I 42 45.290 103.110 140.469 1.00 28.23 S ATOM 57708 SG CYS I 86 13.685 100.699 105.086 1.00 30.29 S ATOM 57757 SG CYS I 89 12.453 104.034 104.137 1.00 33.00 S ATOM 58149 SG CYS I 114 15.548 103.308 102.722 1.00 24.24 S ATOM 58214 SG CYS I 119 15.120 104.143 106.483 1.00 27.51 S ATOM 58436 SG CYS J 7 50.282 96.532 40.931 1.00 5.73 S ATOM 58480 SG CYS J 10 49.580 95.288 37.406 1.00 5.27 S ATOM 59005 SG CYS J 44 47.123 94.583 40.506 1.00 3.00 S ATOM 59015 SG CYS J 45 47.390 97.784 38.653 1.00 1.32 S ATOM 61379 SG CYS L 19 79.277 125.141 57.058 1.00 19.42 S ATOM 61411 SG CYS L 22 79.102 128.013 54.800 1.00 22.23 S ATOM 61641 SG CYS L 36 82.299 127.380 56.186 1.00 24.01 S ATOM 61690 SG CYS L 39 79.211 128.451 58.605 1.00 24.58 S ATOM 62152 SG CYS M 26 84.507 99.820 134.193 1.00 34.19 S ATOM 62196 SG CYS M 29 88.184 99.121 133.363 1.00 31.11 S ATOM 62514 SG CYS M 50 86.096 96.385 134.116 1.00 33.14 S ATOM 62554 SG CYS M 53 86.830 98.751 137.025 1.00 32.93 S Time building chain proxies: 30.27, per 1000 atoms: 0.33 Number of scatterers: 92036 At special positions: 0 Unit cell: (173.25, 153.3, 222.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 9 29.99 S 277 16.00 P 102 15.00 Mg 1 11.99 O 8990 8.00 N 8183 7.00 C 29355 6.00 H 45119 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 Atom "ATOM 63328 O5' DA N 15 .*. O " rejected from bonding due to valence issues. Atom "ATOM 63328 O5' DA N 15 .*. O " rejected from bonding due to valence issues. Atom "ATOM 63328 O5' DA N 15 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 63.60 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 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " 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 M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 50 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 29 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 26 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 53 " Number of angles added : 51 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10560 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 78 sheets defined 34.3% alpha, 22.6% beta 44 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 35.55 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.744A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.773A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.957A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.658A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.895A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.655A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.049A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 4.136A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.776A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.515A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.892A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.684A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) 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 1189 through 1198 removed outlier: 3.614A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A1198 " --> pdb=" O ASN A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.571A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1240 through 1243 removed outlier: 3.956A pdb=" N LEU A1243 " --> pdb=" O GLY A1240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1240 through 1243' Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 3.998A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 4.059A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.813A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.753A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'B' and resid 18 through 37 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 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.543A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.691A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.826A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.702A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.684A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.529A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.817A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.832A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.529A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 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 27 through 41 removed outlier: 3.538A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 269 Processing helix chain 'D' and resid 23 through 28 removed outlier: 4.106A pdb=" N THR D 28 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 90 removed outlier: 4.076A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.756A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.501A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.524A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.119A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 63 through 68 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.731A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.040A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 14 through 29 removed outlier: 3.779A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 500 through 505 Processing helix chain 'b' and resid 508 through 525 Processing helix chain 'b' and resid 538 through 552 Processing helix chain 'b' and resid 574 through 576 No H-bonds generated for 'chain 'b' and resid 574 through 576' Processing helix chain 'b' and resid 577 through 589 Processing helix chain 'b' and resid 606 through 617 Processing helix chain 'b' and resid 624 through 631 Processing helix chain 'b' and resid 648 through 652 Processing helix chain 'b' and resid 656 through 663 Processing helix chain 'b' and resid 681 through 693 removed outlier: 4.161A pdb=" N LEU b 685 " --> pdb=" O ASN b 681 " (cutoff:3.500A) Processing helix chain 'b' and resid 699 through 714 removed outlier: 5.429A 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 720 through 739 Processing helix chain 'b' and resid 769 through 782 Processing helix chain 'b' and resid 782 through 790 removed outlier: 3.697A pdb=" N TYR b 786 " --> pdb=" O SER b 782 " (cutoff:3.500A) Processing helix chain 'b' and resid 794 through 808 removed outlier: 4.210A pdb=" N GLY b 798 " --> pdb=" O GLN b 794 " (cutoff:3.500A) Processing helix chain 'b' and resid 808 through 814 removed outlier: 3.959A pdb=" N PHE b 812 " --> pdb=" O HIS b 808 " (cutoff:3.500A) Processing helix chain 'b' and resid 834 through 837 Processing helix chain 'b' and resid 838 through 855 Processing helix chain 'b' and resid 864 through 878 Processing helix chain 'b' and resid 890 through 892 No H-bonds generated for 'chain 'b' and resid 890 through 892' Processing helix chain 'b' and resid 893 through 904 removed outlier: 3.982A pdb=" N LEU b 897 " --> pdb=" O SER b 893 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP b 904 " --> pdb=" O ARG b 900 " (cutoff:3.500A) Processing helix chain 'b' and resid 937 through 949 removed outlier: 3.917A pdb=" N ASP b 941 " --> pdb=" O ASN b 937 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA b 948 " --> pdb=" O ALA b 944 " (cutoff:3.500A) Processing helix chain 'b' and resid 967 through 988 removed outlier: 3.532A pdb=" N LYS b 971 " --> pdb=" O THR b 967 " (cutoff:3.500A) Processing helix chain 'b' and resid 997 through 1003 Processing helix chain 'b' and resid 1016 through 1022 Processing helix chain 'b' and resid 1387 through 1399 removed outlier: 3.675A pdb=" N LEU b1399 " --> pdb=" O ALA b1395 " (cutoff:3.500A) Processing helix chain 'd' and resid 250 through 254 Processing helix chain 'd' and resid 366 through 370 removed outlier: 3.969A pdb=" N GLN d 370 " --> pdb=" O LEU d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 986 through 990 Processing helix chain 'd' and resid 1044 through 1062 Processing helix chain 'd' and resid 1069 through 1075 Processing helix chain 'd' and resid 1091 through 1096 Processing helix chain 'd' and resid 1097 through 1100 removed outlier: 4.081A pdb=" N ILE d1100 " --> pdb=" O PHE d1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 1097 through 1100' Processing helix chain 'd' and resid 1101 through 1109 Processing helix chain 'd' and resid 1125 through 1139 removed outlier: 3.649A pdb=" N LEU d1129 " --> pdb=" O THR d1125 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE d1139 " --> pdb=" O GLU d1135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.272A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.798A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.693A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 7.501A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.911A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.698A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.176A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.176A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604 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=AB6, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB8, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB9, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.748A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.516A pdb=" N THR A1164 " --> pdb=" O GLN A1299 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1246 through 1247 removed outlier: 3.602A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC4, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 8.315A pdb=" N GLY A1409 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.577A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 removed outlier: 11.046A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC8, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.706A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AD1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD2, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AD3, first strand: chain 'B' and resid 206 through 208 removed outlier: 4.302A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 257 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.530A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.758A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.758A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.286A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE3, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.554A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AE5, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE6, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.512A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.977A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE9, 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: 6.387A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.538A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 149 through 153 removed outlier: 6.688A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AF4, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AF5, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.614A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 35 through 40 Processing sheet with id=AF8, first strand: chain 'a' and resid 30 through 32 Processing sheet with id=AF9, first strand: chain 'a' and resid 36 through 38 removed outlier: 7.453A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'a' and resid 46 through 51 removed outlier: 3.586A pdb=" N THR a 48 " --> pdb=" O GLY a 62 " (cutoff:3.500A) removed outlier: 6.212A 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=AG2, first strand: chain 'a' and resid 102 through 107 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=AG3, first strand: chain 'a' and resid 144 through 149 removed outlier: 6.762A pdb=" N GLY a 162 " --> pdb=" O TYR a 145 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS a 147 " --> pdb=" O ALA a 160 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA a 160 " --> pdb=" O HIS a 147 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N MET a 149 " --> pdb=" O LEU a 158 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU a 158 " --> pdb=" O MET a 149 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 191 through 194 removed outlier: 6.511A pdb=" N LEU a 213 " --> pdb=" O LEU a 223 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 248 through 253 removed outlier: 3.791A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 298 through 299 removed outlier: 6.003A pdb=" N ILE a 316 " --> pdb=" O MET a 329 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET a 329 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL a 318 " --> pdb=" O ILE a 327 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 594 through 596 removed outlier: 6.301A pdb=" N THR b 569 " --> pdb=" O LEU b 621 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N THR b 623 " --> pdb=" O THR b 569 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE b 571 " --> pdb=" O THR b 623 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE b 529 " --> pdb=" O LEU b 743 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 759 through 765 removed outlier: 6.848A pdb=" N ASN b 760 " --> pdb=" O VAL b 959 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ARG b 961 " --> pdb=" O ASN b 760 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN b 762 " --> pdb=" O ARG b 961 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU b 963 " --> pdb=" O GLN b 762 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU b 764 " --> pdb=" O LEU b 963 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL b 929 " --> pdb=" O TYR b 960 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU b 962 " --> pdb=" O VAL b 929 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE b 931 " --> pdb=" O LEU b 962 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU b 883 " --> pdb=" O LEU b 911 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 1004 through 1009 removed outlier: 6.712A pdb=" N GLY d1031 " --> pdb=" O ASN d1005 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE d1007 " --> pdb=" O LEU d1029 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU d1029 " --> pdb=" O PHE d1007 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N HIS d1009 " --> pdb=" O SER d1027 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER d1027 " --> pdb=" O HIS d1009 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER d1027 " --> pdb=" O VAL d1040 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL d1040 " --> pdb=" O SER d1027 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU d1029 " --> pdb=" O GLY d1038 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY d1038 " --> pdb=" O LEU d1029 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU d1039 " --> pdb=" O THR d 8 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N THR d 8 " --> pdb=" O LEU d1039 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR d1041 " --> pdb=" O VAL d 6 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL d 6 " --> pdb=" O THR d1041 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'd' and resid 15 through 21 removed outlier: 6.228A pdb=" N VAL d 43 " --> pdb=" O PRO d 51 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 61 through 67 removed outlier: 3.861A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA d 86 " --> pdb=" O HIS d 105 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS d 105 " --> pdb=" O ALA d 86 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE d 88 " --> pdb=" O ARG d 103 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 121 through 124 Processing sheet with id=AH4, first strand: chain 'd' and resid 164 through 169 removed outlier: 6.673A pdb=" N VAL d 181 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL d 167 " --> pdb=" O CYS d 179 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE d 169 " --> pdb=" O THR d 177 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR d 177 " --> pdb=" O PHE d 169 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 164 through 169 removed outlier: 6.673A pdb=" N VAL d 181 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL d 167 " --> pdb=" O CYS d 179 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE d 169 " --> pdb=" O THR d 177 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR d 177 " --> pdb=" O PHE d 169 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG d 188 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 218 through 221 Processing sheet with id=AH7, first strand: chain 'd' and resid 258 through 263 removed outlier: 4.341A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU d 280 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU d 304 " --> pdb=" O LEU d 280 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET d 282 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL d 302 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU d 284 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU d 300 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU d 286 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 313 through 318 removed outlier: 6.695A pdb=" N VAL d 321 " --> pdb=" O LEU d 317 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER d 331 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR d 352 " --> pdb=" O SER d 331 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU d 333 " --> pdb=" O MET d 350 " (cutoff:3.500A) Processing sheet with id=AH9, 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=AI1, 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: 4.245A 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=AI2, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.376A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.546A 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=AI3, first strand: chain 'd' and resid 872 through 876 removed outlier: 4.115A pdb=" N SER d 872 " --> pdb=" O SER d 883 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL d 888 " --> pdb=" O ASN d 904 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN d 904 " --> pdb=" O VAL d 888 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'd' and resid 911 through 917 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) Processing sheet with id=AI5, first strand: chain 'd' and resid 954 through 959 removed outlier: 3.663A pdb=" N ALA d 956 " --> pdb=" O ALA d 968 " (cutoff:3.500A) removed outlier: 3.675A 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) Processing sheet with id=AI6, first strand: chain 'd' and resid 1076 through 1078 1939 hydrogen bonds defined for protein. 5298 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: 43.92 Time building geometry restraints manager: 66.76 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: 45029 1.02 - 1.22: 170 1.22 - 1.42: 19976 1.42 - 1.62: 27531 1.62 - 1.82: 432 Bond restraints: 93138 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 6.72e+01 bond pdb=" ND2 ASN a 33 " pdb="HD22 ASN a 33 " ideal model delta sigma weight residual 0.860 0.981 -0.121 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 3.60e+01 bond pdb=" ND2 ASN d1049 " pdb="HD21 ASN d1049 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" ND2 ASN d1049 " pdb="HD22 ASN d1049 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 93133 not shown) Histogram of bond angle deviations from ideal: 78.53 - 94.98: 142 94.98 - 111.43: 101622 111.43 - 127.89: 65395 127.89 - 144.34: 722 144.34 - 160.79: 13 Bond angle restraints: 167894 Sorted by residual: angle pdb=" CG ARG A1286 " pdb=" CD ARG A1286 " pdb=" NE ARG A1286 " ideal model delta sigma weight residual 112.00 160.79 -48.79 2.20e+00 2.07e-01 4.92e+02 angle pdb=" CG ARG A 958 " pdb=" CD ARG A 958 " pdb=" NE ARG A 958 " ideal model delta sigma weight residual 112.00 159.14 -47.14 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 114.10 150.96 -36.86 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 114.10 150.50 -36.40 2.00e+00 2.50e-01 3.31e+02 angle pdb=" CA LYS A 105 " pdb=" CB LYS A 105 " pdb=" CG LYS A 105 " ideal model delta sigma weight residual 114.10 148.82 -34.72 2.00e+00 2.50e-01 3.01e+02 ... (remaining 167889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 42218 36.00 - 72.00: 1346 72.00 - 108.00: 49 108.00 - 144.00: 1 144.00 - 180.00: 4 Dihedral angle restraints: 43618 sinusoidal: 24662 harmonic: 18956 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 -180.00 180.00 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 180.00 125.58 54.42 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 180.00 128.62 51.38 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 43615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.594: 7291 0.594 - 1.187: 9 1.187 - 1.781: 4 1.781 - 2.375: 4 2.375 - 2.969: 2 Chirality restraints: 7310 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 2.20e+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 7307 not shown) Planarity restraints: 13510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 388 " 0.094 2.00e-02 2.50e+03 6.52e-02 1.27e+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 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 388 " -0.022 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 " 0.026 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 6.29e-02 1.19e+02 pdb=" CG PHE A 397 " -0.169 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 " 0.000 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 " -0.008 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 6.14e-02 1.13e+02 pdb=" CG PHE A 112 " 0.163 2.00e-02 2.50e+03 pdb=" CD1 PHE A 112 " -0.119 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 " -0.003 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 " 0.005 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 13507 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.27: 22 1.27 - 2.10: 2501 2.10 - 2.94: 249034 2.94 - 3.77: 407923 3.77 - 4.60: 712091 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1371571 Sorted by model distance: nonbonded pdb=" C5' DT N 16 " pdb="HD22 LEU b1004 " model vdw 0.438 2.920 nonbonded pdb=" OP1 DA T 42 " pdb=" CB ARG b 865 " model vdw 0.542 3.100 nonbonded pdb=" CZ ARG B 425 " pdb="HD21 ASN b 999 " model vdw 0.565 2.750 nonbonded pdb="HH12 ARG B 425 " pdb=" ND2 ASN b 999 " model vdw 0.601 2.600 nonbonded pdb=" NH1 ARG B 425 " pdb=" ND2 ASN b 999 " model vdw 0.647 3.100 ... (remaining 1371566 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.020 Extract box with map and model: 14.460 Check model and map are aligned: 1.000 Set scattering table: 0.670 Process input model: 294.620 Find NCS groups from input model: 1.230 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: 0.020 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 320.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 : 0.011 0.246 48019 Z= 0.698 Angle : 1.686 48.795 65300 Z= 0.850 Chirality : 0.103 2.969 7310 Planarity : 0.009 0.177 8089 Dihedral : 16.154 179.995 18448 Min Nonbonded Distance : 0.542 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.08 % Allowed : 0.99 % Favored : 98.93 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.26 (0.11), residues: 5558 helix: -0.47 (0.12), residues: 1734 sheet: -0.86 (0.15), residues: 1134 loop : -0.97 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP b 589 HIS 0.058 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) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 1056 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1052 time to evaluate : 5.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7361 (mtm-85) REVERT: A 532 ARG cc_start: 0.7899 (ptt90) cc_final: 0.7682 (ptt-90) REVERT: A 715 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6683 (mm-30) REVERT: A 779 ILE cc_start: 0.8762 (tp) cc_final: 0.8470 (mm) REVERT: A 869 GLU cc_start: 0.7101 (pt0) cc_final: 0.6900 (pt0) REVERT: A 1027 ASP cc_start: 0.8296 (p0) cc_final: 0.8063 (p0) REVERT: A 1158 LEU cc_start: 0.8663 (tt) cc_final: 0.8344 (tt) REVERT: A 1166 LEU cc_start: 0.8254 (tp) cc_final: 0.7838 (tp) REVERT: A 1261 ILE cc_start: 0.7915 (tp) cc_final: 0.7696 (tp) REVERT: A 1337 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 1398 LEU cc_start: 0.8852 (mp) cc_final: 0.8491 (mt) REVERT: A 1441 GLU cc_start: 0.7538 (tp30) cc_final: 0.7272 (mm-30) REVERT: A 1460 LEU cc_start: 0.8464 (mt) cc_final: 0.8188 (mp) REVERT: B 91 ILE cc_start: 0.8806 (pt) cc_final: 0.8604 (pt) REVERT: B 94 SER cc_start: 0.8437 (p) cc_final: 0.8169 (t) REVERT: B 112 GLU cc_start: 0.7471 (tt0) cc_final: 0.7143 (tt0) REVERT: B 309 PHE cc_start: 0.6834 (t80) cc_final: 0.6542 (t80) REVERT: B 724 TYR cc_start: 0.8080 (m-10) cc_final: 0.7863 (m-10) REVERT: B 728 MET cc_start: 0.8133 (mtm) cc_final: 0.7800 (mtm) REVERT: B 731 GLN cc_start: 0.8302 (mt0) cc_final: 0.8096 (mt0) REVERT: C 166 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7973 (mtpt) REVERT: E 32 GLU cc_start: 0.6493 (pt0) cc_final: 0.6293 (pt0) REVERT: E 72 MET cc_start: 0.7974 (ttp) cc_final: 0.7689 (ttp) REVERT: E 172 ARG cc_start: 0.7999 (mmt90) cc_final: 0.7630 (mtt90) REVERT: E 186 LYS cc_start: 0.7713 (pttt) cc_final: 0.7486 (pttm) REVERT: F 112 ASP cc_start: 0.7791 (p0) cc_final: 0.7576 (p0) REVERT: H 130 ASN cc_start: 0.7049 (m-40) cc_final: 0.6706 (m110) REVERT: J 41 LYS cc_start: 0.7170 (mmtm) cc_final: 0.6939 (mtpt) REVERT: a 90 ILE cc_start: 0.8079 (mm) cc_final: 0.7748 (mt) REVERT: b 752 MET cc_start: 0.4981 (ptp) cc_final: 0.4638 (mmm) outliers start: 4 outliers final: 1 residues processed: 1055 average time/residue: 1.4425 time to fit residues: 2365.4451 Evaluate side-chains 734 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 733 time to evaluate : 5.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 477 optimal weight: 20.0000 chunk 428 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 288 optimal weight: 40.0000 chunk 228 optimal weight: 0.8980 chunk 442 optimal weight: 0.5980 chunk 171 optimal weight: 0.4980 chunk 269 optimal weight: 1.9990 chunk 329 optimal weight: 50.0000 chunk 513 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 260 GLN D 128 GLN E 133 GLN a 180 HIS a 326 GLN d 93 GLN d 374 GLN d 877 ASN d 908 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 48019 Z= 0.266 Angle : 0.676 14.939 65300 Z= 0.359 Chirality : 0.053 1.801 7310 Planarity : 0.006 0.130 8089 Dihedral : 14.057 178.017 7273 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 1.01 % Allowed : 7.27 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.73 (0.11), residues: 5558 helix: 0.32 (0.12), residues: 1708 sheet: -0.81 (0.15), residues: 1144 loop : -0.76 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 835 HIS 0.007 0.001 HIS B 387 PHE 0.025 0.002 PHE A 112 TYR 0.039 0.002 TYR B 388 ARG 0.014 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 822 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 772 time to evaluate : 5.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 ILE cc_start: 0.8729 (tp) cc_final: 0.8499 (mm) REVERT: A 914 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8056 (tttt) REVERT: A 1337 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 1398 LEU cc_start: 0.9021 (mp) cc_final: 0.8638 (mt) REVERT: B 94 SER cc_start: 0.8337 (p) cc_final: 0.8088 (t) REVERT: B 98 HIS cc_start: 0.7390 (t-90) cc_final: 0.7122 (t70) REVERT: B 112 GLU cc_start: 0.7666 (tt0) cc_final: 0.7272 (tt0) REVERT: B 169 ARG cc_start: 0.7106 (mmt180) cc_final: 0.6891 (tpt170) REVERT: B 239 MET cc_start: 0.6454 (tpp) cc_final: 0.6213 (ttt) REVERT: B 497 LYS cc_start: 0.7385 (tptp) cc_final: 0.7132 (tptt) REVERT: B 547 GLU cc_start: 0.6457 (tm-30) cc_final: 0.6203 (tm-30) REVERT: B 654 GLN cc_start: 0.7614 (tp40) cc_final: 0.7343 (tp40) REVERT: B 683 GLN cc_start: 0.7241 (tp-100) cc_final: 0.7003 (mm-40) REVERT: C 166 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8087 (mtpt) REVERT: C 228 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7348 (ttm110) REVERT: E 128 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7235 (mt-10) REVERT: E 186 LYS cc_start: 0.8089 (pttt) cc_final: 0.7733 (pttm) REVERT: F 112 ASP cc_start: 0.7841 (p0) cc_final: 0.7571 (p0) REVERT: b 752 MET cc_start: 0.5054 (ptp) cc_final: 0.4636 (mmm) REVERT: b 771 GLU cc_start: 0.5917 (mp0) cc_final: 0.5706 (mp0) REVERT: b 842 ILE cc_start: 0.7102 (mm) cc_final: 0.6846 (mt) outliers start: 50 outliers final: 21 residues processed: 795 average time/residue: 1.3524 time to fit residues: 1670.4222 Evaluate side-chains 717 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 695 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain b residue 699 THR Chi-restraints excluded: chain b residue 869 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 285 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 427 optimal weight: 20.0000 chunk 349 optimal weight: 0.3980 chunk 141 optimal weight: 0.9990 chunk 514 optimal weight: 9.9990 chunk 555 optimal weight: 9.9990 chunk 457 optimal weight: 8.9990 chunk 509 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 412 optimal weight: 20.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 861 GLN A1077 ASN A1332 GLN B 145 GLN ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN E 107 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN a 79 GLN a 326 GLN b 773 HIS b 974 HIS d 907 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.156 48019 Z= 0.593 Angle : 0.721 11.323 65300 Z= 0.382 Chirality : 0.056 1.632 7310 Planarity : 0.006 0.119 8089 Dihedral : 14.052 178.954 7272 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.47 % Allowed : 8.66 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.80 (0.11), residues: 5558 helix: 0.27 (0.12), residues: 1736 sheet: -0.74 (0.15), residues: 1122 loop : -0.89 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP d 207 HIS 0.011 0.002 HIS A 84 PHE 0.042 0.002 PHE C 63 TYR 0.024 0.002 TYR B1048 ARG 0.016 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 824 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 751 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 CYS cc_start: 0.7691 (m) cc_final: 0.7370 (m) REVERT: A 249 ILE cc_start: 0.8894 (mm) cc_final: 0.8609 (mm) REVERT: A 514 GLU cc_start: 0.8283 (tt0) cc_final: 0.8025 (tt0) REVERT: A 964 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7201 (mm-30) REVERT: A 1129 ASN cc_start: 0.8547 (p0) cc_final: 0.8278 (p0) REVERT: A 1337 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 1341 VAL cc_start: 0.8677 (p) cc_final: 0.8340 (m) REVERT: A 1398 LEU cc_start: 0.8981 (mp) cc_final: 0.8631 (mt) REVERT: A 1423 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7129 (p0) REVERT: B 36 GLU cc_start: 0.7552 (tp30) cc_final: 0.7191 (tp30) REVERT: B 94 SER cc_start: 0.8419 (p) cc_final: 0.8142 (t) REVERT: B 98 HIS cc_start: 0.7678 (t-90) cc_final: 0.7325 (t70) REVERT: B 112 GLU cc_start: 0.7664 (tt0) cc_final: 0.7314 (tt0) REVERT: B 200 MET cc_start: 0.7334 (tpp) cc_final: 0.7102 (mmm) REVERT: B 222 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8146 (mtt180) REVERT: B 463 ARG cc_start: 0.7551 (ptt90) cc_final: 0.7069 (ptt180) REVERT: B 1091 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8504 (ttp80) REVERT: C 145 GLN cc_start: 0.6427 (pt0) cc_final: 0.6067 (mt0) REVERT: C 166 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8181 (mtpt) REVERT: C 228 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7744 (ttm110) REVERT: E 125 TYR cc_start: 0.6787 (m-10) cc_final: 0.6571 (m-10) REVERT: F 112 ASP cc_start: 0.8076 (p0) cc_final: 0.7796 (p0) REVERT: K 110 LYS cc_start: 0.8325 (tppt) cc_final: 0.8091 (ttmm) REVERT: b 752 MET cc_start: 0.5040 (ptp) cc_final: 0.4568 (mmm) outliers start: 73 outliers final: 48 residues processed: 790 average time/residue: 1.3722 time to fit residues: 1681.4943 Evaluate side-chains 760 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 711 time to evaluate : 5.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain b residue 699 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 507 optimal weight: 0.8980 chunk 386 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 56 optimal weight: 0.0770 chunk 245 optimal weight: 0.9980 chunk 345 optimal weight: 0.5980 chunk 515 optimal weight: 10.0000 chunk 546 optimal weight: 9.9990 chunk 269 optimal weight: 0.5980 chunk 488 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 950 ASN A1332 GLN B 500 GLN B 741 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 48019 Z= 0.163 Angle : 0.553 11.469 65300 Z= 0.293 Chirality : 0.050 1.627 7310 Planarity : 0.004 0.068 8089 Dihedral : 13.890 179.581 7272 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.97 % Allowed : 9.73 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.43 (0.11), residues: 5558 helix: 0.72 (0.12), residues: 1739 sheet: -0.68 (0.15), residues: 1116 loop : -0.69 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 207 HIS 0.005 0.001 HIS C 66 PHE 0.021 0.001 PHE A 112 TYR 0.012 0.001 TYR A1197 ARG 0.006 0.000 ARG a 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 800 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 752 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: A 109 CYS cc_start: 0.7572 (m) cc_final: 0.7211 (m) REVERT: A 249 ILE cc_start: 0.8851 (mm) cc_final: 0.8505 (mm) REVERT: A 514 GLU cc_start: 0.8160 (tt0) cc_final: 0.7917 (tt0) REVERT: A 958 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7547 (mtp85) REVERT: A 1129 ASN cc_start: 0.8427 (p0) cc_final: 0.8162 (p0) REVERT: A 1337 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 1398 LEU cc_start: 0.9059 (mp) cc_final: 0.8729 (mt) REVERT: B 36 GLU cc_start: 0.7509 (tp30) cc_final: 0.7131 (tp30) REVERT: B 98 HIS cc_start: 0.7582 (t-90) cc_final: 0.7253 (t70) REVERT: B 112 GLU cc_start: 0.7754 (tt0) cc_final: 0.7421 (tt0) REVERT: B 282 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7985 (ttt90) REVERT: B 296 GLU cc_start: 0.6902 (mp0) cc_final: 0.6647 (mp0) REVERT: B 391 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8131 (mtpt) REVERT: C 145 GLN cc_start: 0.6400 (pt0) cc_final: 0.6088 (mt0) REVERT: C 166 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8127 (mtpt) REVERT: C 254 LYS cc_start: 0.8572 (pttp) cc_final: 0.8350 (ttpp) REVERT: E 125 TYR cc_start: 0.6580 (m-10) cc_final: 0.6126 (m-10) REVERT: F 112 ASP cc_start: 0.7940 (p0) cc_final: 0.7661 (p0) REVERT: H 106 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8580 (p) REVERT: K 110 LYS cc_start: 0.8321 (tppt) cc_final: 0.8082 (ttmm) REVERT: b 752 MET cc_start: 0.5005 (ptp) cc_final: 0.4545 (mmm) outliers start: 48 outliers final: 36 residues processed: 775 average time/residue: 1.3680 time to fit residues: 1642.8555 Evaluate side-chains 755 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 718 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain b residue 699 THR Chi-restraints excluded: chain b residue 770 ASP Chi-restraints excluded: chain d residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 454 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 406 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 466 optimal weight: 10.0000 chunk 377 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 490 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 502 ASN A 950 ASN A1332 GLN ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN a 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 48019 Z= 0.435 Angle : 0.608 11.511 65300 Z= 0.322 Chirality : 0.052 1.610 7310 Planarity : 0.005 0.089 8089 Dihedral : 13.854 179.459 7272 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.55 % Allowed : 9.79 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.37 (0.11), residues: 5558 helix: 0.75 (0.12), residues: 1738 sheet: -0.56 (0.15), residues: 1152 loop : -0.70 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 203 HIS 0.009 0.001 HIS A 685 PHE 0.023 0.002 PHE C 229 TYR 0.018 0.002 TYR A 413 ARG 0.010 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 820 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 743 time to evaluate : 5.627 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: 0.8162 (tppt) cc_final: 0.7928 (ttmm) REVERT: A 249 ILE cc_start: 0.8863 (mm) cc_final: 0.8571 (mm) REVERT: A 514 GLU cc_start: 0.8288 (tt0) cc_final: 0.8018 (tt0) REVERT: A 958 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7615 (mtp85) REVERT: A 1129 ASN cc_start: 0.8486 (p0) cc_final: 0.8200 (p0) REVERT: A 1337 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 1398 LEU cc_start: 0.9055 (mp) cc_final: 0.8720 (mt) REVERT: A 1423 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7033 (p0) REVERT: B 36 GLU cc_start: 0.7552 (tp30) cc_final: 0.7208 (tp30) REVERT: B 98 HIS cc_start: 0.7755 (t-90) cc_final: 0.7407 (t70) REVERT: B 770 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7581 (ttt90) REVERT: B 1091 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8401 (ttp80) REVERT: C 145 GLN cc_start: 0.6541 (pt0) cc_final: 0.6161 (mt0) REVERT: C 166 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8212 (mtpt) REVERT: C 254 LYS cc_start: 0.8600 (pttp) cc_final: 0.8364 (ttpp) REVERT: H 106 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8627 (p) REVERT: b 631 MET cc_start: 0.5588 (mpp) cc_final: 0.5327 (mtm) REVERT: b 752 MET cc_start: 0.5019 (ptp) cc_final: 0.4566 (mmm) outliers start: 77 outliers final: 60 residues processed: 783 average time/residue: 1.3689 time to fit residues: 1666.9455 Evaluate side-chains 781 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 719 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1308 TYR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain b residue 699 THR Chi-restraints excluded: chain b residue 770 ASP Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 855 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 183 optimal weight: 0.9990 chunk 491 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 320 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 546 optimal weight: 9.9990 chunk 453 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 286 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 950 ASN A1078 GLN A1332 GLN B 344 GLN B 741 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 265 HIS E 98 ASN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 48019 Z= 0.190 Angle : 0.539 11.149 65300 Z= 0.284 Chirality : 0.049 1.569 7310 Planarity : 0.004 0.131 8089 Dihedral : 13.750 179.881 7272 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.29 % Allowed : 10.70 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.16 (0.11), residues: 5558 helix: 1.01 (0.13), residues: 1743 sheet: -0.53 (0.15), residues: 1151 loop : -0.58 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 203 HIS 0.006 0.001 HIS a 148 PHE 0.018 0.001 PHE B 320 TYR 0.013 0.001 TYR a 200 ARG 0.008 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 804 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 740 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7952 (pttp) REVERT: A 249 ILE cc_start: 0.8870 (mm) cc_final: 0.8601 (mm) REVERT: A 514 GLU cc_start: 0.8248 (tt0) cc_final: 0.7968 (tt0) REVERT: A 583 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7864 (ttp-110) REVERT: A 917 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: A 1129 ASN cc_start: 0.8359 (p0) cc_final: 0.8080 (p0) REVERT: A 1337 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 1398 LEU cc_start: 0.9054 (mp) cc_final: 0.8712 (mt) REVERT: B 36 GLU cc_start: 0.7522 (tp30) cc_final: 0.7151 (tp30) REVERT: B 98 HIS cc_start: 0.7713 (t-90) cc_final: 0.7391 (t70) REVERT: B 391 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8147 (mtmt) REVERT: B 768 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7777 (mmt90) REVERT: C 145 GLN cc_start: 0.6582 (pt0) cc_final: 0.6163 (mt0) REVERT: C 166 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8166 (mtpt) REVERT: C 254 LYS cc_start: 0.8632 (pttp) cc_final: 0.8369 (ttpp) REVERT: H 106 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8606 (p) REVERT: b 752 MET cc_start: 0.5001 (ptp) cc_final: 0.4540 (mmm) outliers start: 64 outliers final: 46 residues processed: 776 average time/residue: 1.3602 time to fit residues: 1637.2372 Evaluate side-chains 767 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 718 time to evaluate : 5.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1308 TYR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain a residue 106 GLN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain b residue 770 ASP Chi-restraints excluded: chain d residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 527 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 399 optimal weight: 10.0000 chunk 309 optimal weight: 1.9990 chunk 460 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 chunk 544 optimal weight: 20.0000 chunk 340 optimal weight: 0.9980 chunk 332 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 950 ASN A1078 GLN A1332 GLN B 460 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN G 21 ASN G 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 48019 Z= 0.240 Angle : 0.540 11.217 65300 Z= 0.284 Chirality : 0.049 1.570 7310 Planarity : 0.004 0.094 8089 Dihedral : 13.682 179.285 7272 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.31 % Allowed : 10.96 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.06 (0.11), residues: 5558 helix: 1.10 (0.13), residues: 1750 sheet: -0.48 (0.15), residues: 1153 loop : -0.53 (0.12), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 207 HIS 0.005 0.001 HIS H 133 PHE 0.020 0.001 PHE B 320 TYR 0.023 0.001 TYR E 125 ARG 0.007 0.000 ARG b 683 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 809 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 744 time to evaluate : 5.605 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 42 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7976 (pttp) REVERT: A 249 ILE cc_start: 0.8880 (mm) cc_final: 0.8617 (mm) REVERT: A 514 GLU cc_start: 0.8276 (tt0) cc_final: 0.7981 (tt0) REVERT: A 1129 ASN cc_start: 0.8356 (p0) cc_final: 0.8057 (p0) REVERT: A 1337 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 1398 LEU cc_start: 0.9052 (mp) cc_final: 0.8712 (mt) REVERT: B 36 GLU cc_start: 0.7507 (tp30) cc_final: 0.7138 (tp30) REVERT: B 98 HIS cc_start: 0.7747 (t-90) cc_final: 0.7402 (t70) REVERT: B 391 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8212 (mtpt) REVERT: B 415 VAL cc_start: 0.8171 (t) cc_final: 0.7957 (t) REVERT: B 768 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7790 (mmt90) REVERT: C 145 GLN cc_start: 0.6595 (pt0) cc_final: 0.6262 (mt0) REVERT: C 254 LYS cc_start: 0.8633 (pttp) cc_final: 0.8375 (ttpp) REVERT: H 106 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8579 (p) REVERT: a 347 GLN cc_start: 0.7356 (mp10) cc_final: 0.7008 (mp10) REVERT: b 752 MET cc_start: 0.5017 (ptp) cc_final: 0.4549 (mmm) outliers start: 65 outliers final: 51 residues processed: 780 average time/residue: 1.3660 time to fit residues: 1656.0105 Evaluate side-chains 786 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 733 time to evaluate : 5.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1308 TYR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain a residue 106 GLN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain b residue 770 ASP Chi-restraints excluded: chain d residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 336 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 325 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 428 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 461 GLN A 950 ASN A1078 GLN A1332 GLN ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN G 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 48019 Z= 0.226 Angle : 0.533 11.271 65300 Z= 0.280 Chirality : 0.049 1.563 7310 Planarity : 0.004 0.063 8089 Dihedral : 13.636 179.403 7272 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.21 % Allowed : 11.12 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.01 (0.11), residues: 5558 helix: 1.17 (0.13), residues: 1751 sheet: -0.45 (0.15), residues: 1155 loop : -0.48 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 207 HIS 0.005 0.001 HIS H 133 PHE 0.022 0.001 PHE B 320 TYR 0.022 0.001 TYR E 125 ARG 0.009 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 813 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 753 time to evaluate : 5.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ILE cc_start: 0.8900 (mm) cc_final: 0.8633 (mm) REVERT: A 514 GLU cc_start: 0.8278 (tt0) cc_final: 0.7960 (tt0) REVERT: A 696 SER cc_start: 0.8685 (p) cc_final: 0.8387 (m) REVERT: A 1129 ASN cc_start: 0.8273 (p0) cc_final: 0.7986 (p0) REVERT: A 1337 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 1398 LEU cc_start: 0.9092 (mp) cc_final: 0.8744 (mt) REVERT: B 36 GLU cc_start: 0.7500 (tp30) cc_final: 0.7149 (tp30) REVERT: B 98 HIS cc_start: 0.7753 (t-90) cc_final: 0.7428 (t70) REVERT: B 107 PRO cc_start: 0.8840 (Cg_endo) cc_final: 0.8597 (Cg_exo) REVERT: B 391 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8231 (mtpt) REVERT: B 415 VAL cc_start: 0.8141 (t) cc_final: 0.7928 (t) REVERT: B 463 ARG cc_start: 0.7566 (ptt90) cc_final: 0.7320 (ptt90) REVERT: C 145 GLN cc_start: 0.6489 (pt0) cc_final: 0.6168 (mt0) REVERT: C 254 LYS cc_start: 0.8643 (pttp) cc_final: 0.8385 (ttpp) REVERT: H 106 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8589 (p) REVERT: a 347 GLN cc_start: 0.7366 (mp10) cc_final: 0.7063 (mp10) REVERT: b 752 MET cc_start: 0.4965 (ptp) cc_final: 0.4590 (mmm) outliers start: 60 outliers final: 50 residues processed: 785 average time/residue: 1.3814 time to fit residues: 1680.9142 Evaluate side-chains 790 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 739 time to evaluate : 5.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1308 TYR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain a residue 106 GLN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain b residue 869 ASP Chi-restraints excluded: chain d residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 495 optimal weight: 20.0000 chunk 521 optimal weight: 0.9980 chunk 475 optimal weight: 10.0000 chunk 507 optimal weight: 9.9990 chunk 305 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 398 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 458 optimal weight: 10.0000 chunk 479 optimal weight: 20.0000 chunk 505 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 461 GLN A 576 GLN A 711 GLN A 950 ASN A1078 GLN A1332 GLN B 23 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS a 326 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.146 48019 Z= 0.616 Angle : 0.675 11.607 65300 Z= 0.355 Chirality : 0.056 1.569 7310 Planarity : 0.006 0.120 8089 Dihedral : 13.784 179.303 7272 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.43 % Allowed : 10.86 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.29 (0.11), residues: 5558 helix: 0.78 (0.12), residues: 1753 sheet: -0.48 (0.15), residues: 1149 loop : -0.64 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP d 207 HIS 0.016 0.002 HIS B 350 PHE 0.026 0.002 PHE B 34 TYR 0.023 0.002 TYR B 160 ARG 0.014 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 803 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 732 time to evaluate : 5.637 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 249 ILE cc_start: 0.8964 (mm) cc_final: 0.8685 (mm) REVERT: A 514 GLU cc_start: 0.8367 (tt0) cc_final: 0.8061 (tt0) REVERT: A 696 SER cc_start: 0.8764 (p) cc_final: 0.8448 (m) REVERT: A 735 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7044 (tp40) REVERT: A 1129 ASN cc_start: 0.8487 (p0) cc_final: 0.8149 (p0) REVERT: A 1337 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 1398 LEU cc_start: 0.9027 (mp) cc_final: 0.8707 (mt) REVERT: A 1423 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7113 (p0) REVERT: B 36 GLU cc_start: 0.7584 (tp30) cc_final: 0.7266 (tp30) REVERT: B 94 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8153 (t) REVERT: B 309 PHE cc_start: 0.6965 (t80) cc_final: 0.6701 (t80) REVERT: B 415 VAL cc_start: 0.8220 (t) cc_final: 0.8009 (t) REVERT: B 463 ARG cc_start: 0.7615 (ptt90) cc_final: 0.7166 (ptt180) REVERT: C 145 GLN cc_start: 0.6656 (pt0) cc_final: 0.6277 (mt0) REVERT: C 254 LYS cc_start: 0.8656 (pttp) cc_final: 0.8389 (ttpp) REVERT: a 347 GLN cc_start: 0.7465 (mp10) cc_final: 0.7177 (mp10) REVERT: b 752 MET cc_start: 0.4994 (ptp) cc_final: 0.4655 (mmm) outliers start: 71 outliers final: 60 residues processed: 774 average time/residue: 1.3688 time to fit residues: 1641.1856 Evaluate side-chains 780 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 717 time to evaluate : 5.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1079 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain a residue 106 GLN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain b residue 770 ASP Chi-restraints excluded: chain b residue 869 ASP Chi-restraints excluded: chain d residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 333 optimal weight: 8.9990 chunk 536 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 254 optimal weight: 0.0670 chunk 373 optimal weight: 0.5980 chunk 562 optimal weight: 8.9990 chunk 518 optimal weight: 0.8980 chunk 448 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 346 optimal weight: 4.9990 chunk 274 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 461 GLN A 950 ASN A1078 GLN A1394 ASN ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48019 Z= 0.177 Angle : 0.540 11.332 65300 Z= 0.283 Chirality : 0.049 1.558 7310 Planarity : 0.004 0.081 8089 Dihedral : 13.654 179.956 7272 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.97 % Allowed : 11.70 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.01 (0.11), residues: 5558 helix: 1.09 (0.13), residues: 1757 sheet: -0.43 (0.15), residues: 1154 loop : -0.48 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP d 207 HIS 0.004 0.001 HIS C 60 PHE 0.023 0.001 PHE B 320 TYR 0.013 0.001 TYR I 54 ARG 0.010 0.000 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11116 Ramachandran restraints generated. 5558 Oldfield, 0 Emsley, 5558 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. Evaluate side-chains 791 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 743 time to evaluate : 5.573 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: A 249 ILE cc_start: 0.8947 (mm) cc_final: 0.8697 (mm) REVERT: A 514 GLU cc_start: 0.8277 (tt0) cc_final: 0.7970 (tt0) REVERT: A 696 SER cc_start: 0.8705 (p) cc_final: 0.8410 (m) REVERT: A 735 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7015 (tp40) REVERT: A 1129 ASN cc_start: 0.8257 (p0) cc_final: 0.7920 (p0) REVERT: A 1337 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 1398 LEU cc_start: 0.9051 (mp) cc_final: 0.8727 (mt) REVERT: B 36 GLU cc_start: 0.7495 (tp30) cc_final: 0.7147 (tp30) REVERT: B 94 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.8020 (t) REVERT: B 107 PRO cc_start: 0.8820 (Cg_endo) cc_final: 0.8583 (Cg_exo) REVERT: B 415 VAL cc_start: 0.8120 (t) cc_final: 0.7911 (t) REVERT: B 463 ARG cc_start: 0.7694 (ptt90) cc_final: 0.7189 (ptt180) REVERT: C 145 GLN cc_start: 0.6552 (pt0) cc_final: 0.6174 (mt0) REVERT: C 254 LYS cc_start: 0.8658 (pttp) cc_final: 0.8392 (ttpp) REVERT: E 186 LYS cc_start: 0.8233 (pttt) cc_final: 0.7840 (pttm) REVERT: a 347 GLN cc_start: 0.7334 (mp10) cc_final: 0.7075 (mp10) REVERT: b 752 MET cc_start: 0.4961 (ptp) cc_final: 0.4630 (mmm) outliers start: 48 outliers final: 41 residues processed: 767 average time/residue: 1.3903 time to fit residues: 1662.4988 Evaluate side-chains 766 residues out of total 4979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 723 time to evaluate : 5.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1394 ASN Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 65 LEU 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 90 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain a residue 106 GLN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain b residue 869 ASP Chi-restraints excluded: chain d residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 356 optimal weight: 0.8980 chunk 477 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 413 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 448 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 460 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 950 ASN A1078 GLN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN G 21 ASN a 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.216193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.164480 restraints weight = 139133.484| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.68 r_work: 0.3473 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 48019 Z= 0.266 Angle : 0.620 59.200 65300 Z= 0.340 Chirality : 0.050 1.560 7310 Planarity : 0.004 0.075 8089 Dihedral : 13.649 179.905 7272 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.99 % Allowed : 11.68 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -0.01 (0.11), residues: 5558 helix: 1.09 (0.13), residues: 1757 sheet: -0.42 (0.15), residues: 1154 loop : -0.47 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP d 207 HIS 0.006 0.001 HIS A1220 PHE 0.022 0.001 PHE B 320 TYR 0.015 0.001 TYR I 54 ARG 0.010 0.000 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25573.74 seconds wall clock time: 441 minutes 59.38 seconds (26519.38 seconds total)