Starting phenix.real_space_refine on Sun Jul 28 05:09:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh3_36252/07_2024/8jh3_36252_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh3_36252/07_2024/8jh3_36252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh3_36252/07_2024/8jh3_36252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh3_36252/07_2024/8jh3_36252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh3_36252/07_2024/8jh3_36252_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh3_36252/07_2024/8jh3_36252_neut.cif" } resolution = 3.7 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 312 5.49 5 Mg 1 5.21 5 S 200 5.16 5 C 26369 2.51 5 N 7718 2.21 5 O 8808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 435": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A ARG 727": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 807": "NH1" <-> "NH2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A ARG 881": "NH1" <-> "NH2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A ARG 945": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1025": "NH1" <-> "NH2" Residue "A ARG 1027": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A ARG 1032": "NH1" <-> "NH2" Residue "A ARG 1038": "NH1" <-> "NH2" Residue "A ARG 1041": "NH1" <-> "NH2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1124": "NH1" <-> "NH2" Residue "A ARG 1196": "NH1" <-> "NH2" Residue "A ARG 1201": "NH1" <-> "NH2" Residue "A ARG 1203": "NH1" <-> "NH2" Residue "A ARG 1241": "NH1" <-> "NH2" Residue "A ARG 1243": "NH1" <-> "NH2" Residue "A ARG 1265": "NH1" <-> "NH2" Residue "A ARG 1277": "NH1" <-> "NH2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A ARG 1348": "NH1" <-> "NH2" Residue "A ARG 1369": "NH1" <-> "NH2" Residue "A ARG 1381": "NH1" <-> "NH2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A ARG 1394": "NH1" <-> "NH2" Residue "A ARG 1402": "NH1" <-> "NH2" Residue "A ARG 1425": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 398": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 415": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B ARG 433": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 710": "NH1" <-> "NH2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "B ARG 788": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 848": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 857": "NH1" <-> "NH2" Residue "B ARG 865": "NH1" <-> "NH2" Residue "B ARG 879": "NH1" <-> "NH2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "B ARG 904": "NH1" <-> "NH2" Residue "B ARG 935": "NH1" <-> "NH2" Residue "B ARG 942": "NH1" <-> "NH2" Residue "B ARG 967": "NH1" <-> "NH2" Residue "B ARG 969": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1020": "NH1" <-> "NH2" Residue "B ARG 1038": "NH1" <-> "NH2" Residue "B ARG 1060": "NH1" <-> "NH2" Residue "B ARG 1067": "NH1" <-> "NH2" Residue "B ARG 1094": "NH1" <-> "NH2" Residue "B ARG 1096": "NH1" <-> "NH2" Residue "B ARG 1106": "NH1" <-> "NH2" Residue "B ARG 1108": "NH1" <-> "NH2" Residue "B ARG 1116": "NH1" <-> "NH2" Residue "B ARG 1122": "NH1" <-> "NH2" Residue "B ARG 1124": "NH1" <-> "NH2" Residue "B ARG 1129": "NH1" <-> "NH2" Residue "B ARG 1135": "NH1" <-> "NH2" Residue "B ARG 1150": "NH1" <-> "NH2" Residue "B ARG 1159": "NH1" <-> "NH2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "B ARG 1215": "NH1" <-> "NH2" Residue "B ARG 1220": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "E ARG 6": "NH1" <-> "NH2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E ARG 211": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "G ARG 151": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 144": "NH1" <-> "NH2" Residue "H ARG 145": "NH1" <-> "NH2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I ARG 45": "NH1" <-> "NH2" Residue "I ARG 70": "NH1" <-> "NH2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J ARG 23": "NH1" <-> "NH2" Residue "J ARG 42": "NH1" <-> "NH2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "K ARG 6": "NH1" <-> "NH2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L ARG 62": "NH1" <-> "NH2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a ARG 42": "NH1" <-> "NH2" Residue "a ARG 49": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ARG 69": "NH1" <-> "NH2" Residue "a ARG 72": "NH1" <-> "NH2" Residue "a ARG 83": "NH1" <-> "NH2" Residue "a ARG 116": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 129": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "b ARG 35": "NH1" <-> "NH2" Residue "b ARG 36": "NH1" <-> "NH2" Residue "b ARG 39": "NH1" <-> "NH2" Residue "b ARG 40": "NH1" <-> "NH2" Residue "b ARG 45": "NH1" <-> "NH2" Residue "b ARG 55": "NH1" <-> "NH2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 78": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "c ARG 17": "NH1" <-> "NH2" Residue "c ARG 20": "NH1" <-> "NH2" Residue "c ARG 29": "NH1" <-> "NH2" Residue "c ARG 32": "NH1" <-> "NH2" Residue "c ARG 35": "NH1" <-> "NH2" Residue "c ARG 42": "NH1" <-> "NH2" Residue "c ARG 71": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 81": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 99": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d ARG 99": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 52": "NH1" <-> "NH2" Residue "e ARG 53": "NH1" <-> "NH2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e ARG 69": "NH1" <-> "NH2" Residue "e ARG 72": "NH1" <-> "NH2" Residue "e ARG 83": "NH1" <-> "NH2" Residue "e ARG 116": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "e ARG 129": "NH1" <-> "NH2" Residue "e ARG 131": "NH1" <-> "NH2" Residue "e ARG 134": "NH1" <-> "NH2" Residue "f ARG 35": "NH1" <-> "NH2" Residue "f ARG 36": "NH1" <-> "NH2" Residue "f ARG 39": "NH1" <-> "NH2" Residue "f ARG 40": "NH1" <-> "NH2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f ARG 67": "NH1" <-> "NH2" Residue "f ARG 78": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 95": "NH1" <-> "NH2" Residue "g ARG 17": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g ARG 35": "NH1" <-> "NH2" Residue "g ARG 42": "NH1" <-> "NH2" Residue "g ARG 71": "NH1" <-> "NH2" Residue "g ARG 77": "NH1" <-> "NH2" Residue "g ARG 81": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 99": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 79": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 92": "NH1" <-> "NH2" Residue "h ARG 99": "NH1" <-> "NH2" Time to flip residues: 1.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 43416 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 11120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11120 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1343} Chain breaks: 5 Chain: "B" Number of atoms: 9210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 9210 Classifications: {'peptide': 1155} Link IDs: {'PTRANS': 52, 'TRANS': 1102} Chain breaks: 5 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2897 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 281 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3243 Classifications: {'DNA': 159} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 158} Chain: "a" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "b" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "c" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "d" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "h" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 87.465 57.565 118.205 1.00 56.61 S ATOM 549 SG CYS A 70 90.752 57.042 120.042 1.00 49.09 S ATOM 594 SG CYS A 77 88.770 60.271 120.638 1.00 40.91 S ATOM 829 SG CYS A 107 100.420 86.727 81.557 1.00 95.18 S ATOM 851 SG CYS A 110 102.076 83.418 80.890 1.00 92.30 S ATOM 1157 SG CYS A 148 103.910 86.579 80.056 1.00102.85 S ATOM 1245 SG CYS A 168 100.954 85.595 77.911 1.00 90.43 S ATOM 19862 SG CYS B1163 104.008 61.398 110.969 1.00 50.40 S ATOM 19880 SG CYS B1166 101.900 64.373 109.787 1.00 53.42 S ATOM 20003 SG CYS B1182 100.620 60.867 109.662 1.00 71.56 S ATOM 20026 SG CYS B1185 103.342 61.989 107.184 1.00 76.29 S ATOM 20971 SG CYS C 85 76.115 63.802 186.119 1.00 93.30 S ATOM 20984 SG CYS C 87 74.405 63.510 182.932 1.00103.14 S ATOM 21019 SG CYS C 91 72.625 63.935 186.449 1.00 86.34 S ATOM 21042 SG CYS C 94 74.289 66.959 184.597 1.00 63.81 S ATOM 29128 SG CYS I 75 78.116 159.754 135.942 1.00108.75 S ATOM 29150 SG CYS I 78 74.697 161.152 137.064 1.00110.02 S ATOM 29366 SG CYS I 103 75.507 157.276 137.005 1.00 98.40 S ATOM 29388 SG CYS I 106 75.249 159.521 133.822 1.00105.79 S ATOM 28580 SG CYS I 7 71.221 146.989 91.450 1.00111.89 S ATOM 28766 SG CYS I 29 73.463 144.283 89.467 1.00110.40 S ATOM 28791 SG CYS I 32 71.682 146.030 88.223 1.00117.22 S ATOM 29507 SG CYS J 7 75.595 98.565 178.630 1.00 20.33 S ATOM 29530 SG CYS J 10 77.465 97.811 181.870 1.00 17.54 S ATOM 29806 SG CYS J 44 77.920 101.193 180.013 1.00 28.16 S ATOM 29812 SG CYS J 45 74.840 100.231 182.077 1.00 21.10 S ATOM 30974 SG CYS L 33 43.878 80.128 153.115 1.00 71.01 S ATOM 30989 SG CYS L 36 40.628 79.742 155.016 1.00 85.31 S ATOM 31099 SG CYS L 50 41.846 77.092 152.392 1.00 79.56 S ATOM 31123 SG CYS L 53 40.544 80.540 151.379 1.00 90.45 S Time building chain proxies: 22.62, per 1000 atoms: 0.52 Number of scatterers: 43416 At special positions: 0 Unit cell: (172.78, 173.84, 219.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 200 16.00 P 312 15.00 Mg 1 11.99 O 8808 8.00 N 7718 7.00 C 26369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.56 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " 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 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " Number of angles added : 39 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8718 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 56 sheets defined 44.1% alpha, 16.0% beta 131 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 15.96 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.042A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.864A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.522A pdb=" N GLY A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.534A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.503A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.989A pdb=" N ILE A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.609A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.680A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.504A pdb=" N VAL A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.756A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.540A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.528A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.146A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.663A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.993A pdb=" N LEU A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 947 Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'A' and resid 1006 through 1017 Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.935A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 3.786A pdb=" N ASP A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.631A pdb=" N ALA A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1200 through 1207 removed outlier: 3.626A pdb=" N MET A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.635A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1274 Processing helix chain 'A' and resid 1315 through 1322 Processing helix chain 'A' and resid 1334 through 1343 Processing helix chain 'A' and resid 1343 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 4.070A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1406 removed outlier: 3.521A pdb=" N ARG A1402 " --> pdb=" O GLY A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.973A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.963A pdb=" N ALA A1461 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 51 removed outlier: 5.568A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLN B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 300 through 306 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.721A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.772A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 3.867A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 431 removed outlier: 4.079A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.636A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.311A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.687A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.904A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.572A pdb=" N ILE B 652 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.651A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.576A pdb=" N LEU B 707 " --> pdb=" O PRO B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.654A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.944A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.532A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 264 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.727A pdb=" N LEU D 28 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 95 through 111 Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.710A pdb=" N CYS D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.742A pdb=" N ALA D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.940A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 30 through 35 removed outlier: 3.617A pdb=" N ASP E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.604A pdb=" N ILE G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.587A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.079A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) 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 removed outlier: 3.556A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.782A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'a' and resid 45 through 56 Processing helix chain 'a' and resid 63 through 77 removed outlier: 3.607A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.501A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 3.638A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.502A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.372A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 removed outlier: 3.503A pdb=" N ALA h 107 " --> pdb=" O PRO h 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.082A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 239 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 178 removed outlier: 4.397A pdb=" N LEU A 182 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.909A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 259 " --> pdb=" O ILE A 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.682A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.673A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.773A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.066A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 56 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.838A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.835A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.037A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.299A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 3.720A pdb=" N ARG A1196 " --> pdb=" O GLU A1153 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A1151 " --> pdb=" O GLU A1198 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 3.511A pdb=" N VAL F 133 " --> pdb=" O MET A1447 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY G 59 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 60 removed outlier: 3.505A pdb=" N ILE B 77 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 75 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 60 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.523A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.990A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 231 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.542A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.615A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.615A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL L 29 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU L 42 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.521A pdb=" N MET B 839 " --> pdb=" O VAL B 992 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR B 994 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET B 841 " --> pdb=" O TYR B 994 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.766A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.538A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 6 through 12 removed outlier: 5.486A pdb=" N VAL C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER C 22 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.956A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.769A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.501A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.659A pdb=" N THR D 5 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE5, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.555A pdb=" N PHE E 59 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 79 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE7, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.008A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 4.014A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 14 through 18 removed outlier: 3.688A pdb=" N LYS I 17 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU I 36 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 removed outlier: 3.589A pdb=" N PHE K 58 " --> pdb=" O GLN K 76 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.914A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF5, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AF6, first strand: chain 'c' and resid 42 through 43 removed outlier: 6.989A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AF8, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AF9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.770A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.015A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 1729 hydrogen bonds defined for protein. 4857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 666 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 30.17 Time building geometry restraints manager: 18.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6548 1.30 - 1.43: 12617 1.43 - 1.56: 24724 1.56 - 1.69: 624 1.69 - 1.82: 326 Bond restraints: 44839 Sorted by residual: bond pdb=" C ARG a 52 " pdb=" O ARG a 52 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.15e-02 7.56e+03 3.81e+01 bond pdb=" C GLN c 112 " pdb=" O GLN c 112 " ideal model delta sigma weight residual 1.235 1.295 -0.060 1.20e-02 6.94e+03 2.53e+01 bond pdb=" CA ARG d 33 " pdb=" C ARG d 33 " ideal model delta sigma weight residual 1.524 1.562 -0.039 1.30e-02 5.92e+03 8.82e+00 bond pdb=" N ARG A 45 " pdb=" CA ARG A 45 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.12e+00 bond pdb=" N CYS C 91 " pdb=" CA CYS C 91 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.22e-02 6.72e+03 8.09e+00 ... (remaining 44834 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.75: 2229 105.75 - 112.85: 24159 112.85 - 119.95: 15638 119.95 - 127.05: 18867 127.05 - 134.15: 995 Bond angle restraints: 61888 Sorted by residual: angle pdb=" N VAL a 117 " pdb=" CA VAL a 117 " pdb=" C VAL a 117 " ideal model delta sigma weight residual 113.47 106.27 7.20 1.01e+00 9.80e-01 5.08e+01 angle pdb=" N VAL e 117 " pdb=" CA VAL e 117 " pdb=" C VAL e 117 " ideal model delta sigma weight residual 113.47 107.59 5.88 1.01e+00 9.80e-01 3.39e+01 angle pdb=" C ALA B 62 " pdb=" CA ALA B 62 " pdb=" CB ALA B 62 " ideal model delta sigma weight residual 116.63 110.94 5.69 1.16e+00 7.43e-01 2.40e+01 angle pdb=" C HIS h 49 " pdb=" N PRO h 50 " pdb=" CA PRO h 50 " ideal model delta sigma weight residual 119.47 125.15 -5.68 1.16e+00 7.43e-01 2.40e+01 angle pdb=" CA ALA B 62 " pdb=" C ALA B 62 " pdb=" N GLN B 63 " ideal model delta sigma weight residual 119.63 115.93 3.70 8.10e-01 1.52e+00 2.09e+01 ... (remaining 61883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 24985 35.86 - 71.73: 1542 71.73 - 107.59: 53 107.59 - 143.46: 1 143.46 - 179.32: 2 Dihedral angle restraints: 26583 sinusoidal: 13089 harmonic: 13494 Sorted by residual: dihedral pdb=" C4' DC T 4 " pdb=" C3' DC T 4 " pdb=" O3' DC T 4 " pdb=" P DC T 5 " ideal model delta sinusoidal sigma weight residual -140.00 39.32 -179.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC T 45 " pdb=" C3' DC T 45 " pdb=" O3' DC T 45 " pdb=" P DA T 46 " ideal model delta sinusoidal sigma weight residual -140.00 35.09 -175.09 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP B 176 " pdb=" C ASP B 176 " pdb=" N GLU B 177 " pdb=" CA GLU B 177 " ideal model delta harmonic sigma weight residual -180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 26580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5211 0.045 - 0.090: 1315 0.090 - 0.134: 392 0.134 - 0.179: 34 0.179 - 0.224: 3 Chirality restraints: 6955 Sorted by residual: chirality pdb=" CA LYS g 74 " pdb=" N LYS g 74 " pdb=" C LYS g 74 " pdb=" CB LYS g 74 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE c 111 " pdb=" N ILE c 111 " pdb=" C ILE c 111 " pdb=" CB ILE c 111 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA VAL e 117 " pdb=" N VAL e 117 " pdb=" C VAL e 117 " pdb=" CB VAL e 117 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 6952 not shown) Planarity restraints: 6891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR d 37 " -0.070 2.00e-02 2.50e+03 4.01e-02 3.22e+01 pdb=" CG TYR d 37 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR d 37 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR d 37 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR d 37 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR d 37 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR d 37 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR d 37 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 73 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" CG ASN c 73 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN c 73 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN c 73 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL c 43 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C VAL c 43 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL c 43 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY c 44 " 0.017 2.00e-02 2.50e+03 ... (remaining 6888 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 6 1.90 - 2.65: 565 2.65 - 3.40: 56527 3.40 - 4.15: 108927 4.15 - 4.90: 189296 Nonbonded interactions: 355321 Sorted by model distance: nonbonded pdb=" OP2 DA T -44 " pdb=" NH2 ARG c 32 " model vdw 1.149 2.520 nonbonded pdb=" OP2 DA T -44 " pdb=" CZ ARG c 32 " model vdw 1.258 3.270 nonbonded pdb=" P DA T -44 " pdb=" NH2 ARG c 32 " model vdw 1.483 3.480 nonbonded pdb=" OP2 DA T -44 " pdb=" NH1 ARG c 32 " model vdw 1.486 2.520 nonbonded pdb=" SD MET A 253 " pdb=" N3 DC T 42 " model vdw 1.757 3.480 ... (remaining 355316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 43 through 133) selection = (chain 'e' and resid 43 through 133) } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 25 through 101) } ncs_group { reference = (chain 'c' and resid 17 through 109) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 36 through 123) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.750 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 137.890 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 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 : 0.005 0.071 44839 Z= 0.291 Angle : 0.713 9.176 61888 Z= 0.451 Chirality : 0.044 0.224 6955 Planarity : 0.004 0.062 6891 Dihedral : 19.209 179.320 17865 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 0.35 % Allowed : 0.86 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 4589 helix: 0.14 (0.12), residues: 1833 sheet: -1.12 (0.20), residues: 636 loop : -0.82 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 201 HIS 0.007 0.001 HIS B 996 PHE 0.031 0.002 PHE B 217 TYR 0.070 0.002 TYR d 37 ARG 0.013 0.001 ARG a 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 484 time to evaluate : 5.611 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: A 253 MET cc_start: 0.3187 (tmm) cc_final: 0.2746 (mtm) REVERT: A 282 MET cc_start: 0.5370 (mmp) cc_final: 0.5051 (ppp) REVERT: B 35 LEU cc_start: 0.6786 (mt) cc_final: 0.6584 (mp) REVERT: B 860 MET cc_start: 0.6093 (tmm) cc_final: 0.5719 (tmm) REVERT: B 1082 MET cc_start: 0.8042 (tpp) cc_final: 0.7782 (tpt) REVERT: B 1152 MET cc_start: 0.7166 (mmm) cc_final: 0.6907 (mmm) REVERT: C 81 TYR cc_start: 0.6838 (m-80) cc_final: 0.6609 (m-80) REVERT: D 24 ASN cc_start: 0.3706 (t0) cc_final: 0.3226 (p0) REVERT: h 59 MET cc_start: 0.4852 (tpt) cc_final: 0.4324 (tmm) outliers start: 14 outliers final: 0 residues processed: 496 average time/residue: 0.6343 time to fit residues: 491.1610 Evaluate side-chains 203 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 411 optimal weight: 10.0000 chunk 369 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 381 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 284 optimal weight: 40.0000 chunk 442 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 265 HIS A1393 ASN B 356 HIS B 506 GLN B 708 GLN B 794 ASN B 996 HIS B1104 HIS C 264 ASN D 17 GLN D 46 HIS D 144 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN K 110 ASN b 93 GLN c 110 ASN c 112 GLN d 84 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 44839 Z= 0.360 Angle : 0.707 14.500 61888 Z= 0.374 Chirality : 0.044 0.194 6955 Planarity : 0.006 0.071 6891 Dihedral : 21.378 178.646 8585 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 1.18 % Allowed : 7.17 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 4589 helix: 1.02 (0.12), residues: 1854 sheet: -0.75 (0.20), residues: 643 loop : -0.58 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 18 HIS 0.016 0.002 HIS D 138 PHE 0.026 0.003 PHE D 140 TYR 0.021 0.002 TYR h 42 ARG 0.010 0.001 ARG c 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 5.021 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: A 146 MET cc_start: 0.3675 (mmt) cc_final: 0.3448 (mmt) REVERT: A 253 MET cc_start: 0.3795 (tmm) cc_final: 0.2741 (mtm) REVERT: A 1439 MET cc_start: 0.7978 (ptp) cc_final: 0.7586 (ptp) REVERT: B 860 MET cc_start: 0.6693 (tmm) cc_final: 0.6492 (tmm) REVERT: B 1152 MET cc_start: 0.7393 (mmm) cc_final: 0.7152 (mmm) REVERT: D 24 ASN cc_start: 0.3800 (t0) cc_final: 0.3242 (p0) REVERT: G 35 GLU cc_start: 0.4914 (mt-10) cc_final: 0.3665 (tp30) REVERT: G 153 ASP cc_start: 0.1810 (t0) cc_final: 0.1578 (t0) REVERT: c 41 GLU cc_start: 0.2365 (OUTLIER) cc_final: 0.2145 (pt0) outliers start: 48 outliers final: 25 residues processed: 251 average time/residue: 0.5431 time to fit residues: 229.9424 Evaluate side-chains 204 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 5.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain a residue 120 MET Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 245 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 368 optimal weight: 0.7980 chunk 301 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 443 optimal weight: 20.0000 chunk 478 optimal weight: 30.0000 chunk 394 optimal weight: 9.9990 chunk 439 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 355 optimal weight: 0.8980 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 291 ASN A 314 GLN A 651 GLN B 70 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN D 138 HIS ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN I 31 ASN c 73 ASN c 112 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44839 Z= 0.243 Angle : 0.562 10.758 61888 Z= 0.301 Chirality : 0.040 0.264 6955 Planarity : 0.004 0.053 6891 Dihedral : 21.370 177.623 8585 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 1.28 % Allowed : 8.80 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 4589 helix: 1.49 (0.12), residues: 1855 sheet: -0.52 (0.20), residues: 631 loop : -0.35 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 192 HIS 0.005 0.001 HIS A1290 PHE 0.019 0.002 PHE C 178 TYR 0.013 0.001 TYR H 140 ARG 0.008 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.3799 (mmt) cc_final: 0.3550 (mmt) REVERT: A 253 MET cc_start: 0.4370 (tmm) cc_final: 0.3195 (mtm) REVERT: A 1439 MET cc_start: 0.7945 (ptp) cc_final: 0.7493 (ptp) REVERT: B 699 MET cc_start: 0.8385 (tpp) cc_final: 0.7876 (tpp) REVERT: D 24 ASN cc_start: 0.3738 (t0) cc_final: 0.3144 (p0) REVERT: G 35 GLU cc_start: 0.5001 (mt-10) cc_final: 0.4655 (tp30) REVERT: g 41 GLU cc_start: 0.2826 (OUTLIER) cc_final: 0.2311 (mt-10) outliers start: 52 outliers final: 22 residues processed: 230 average time/residue: 0.5424 time to fit residues: 213.3827 Evaluate side-chains 190 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 4.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain g residue 41 GLU Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 437 optimal weight: 30.0000 chunk 333 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 211 optimal weight: 0.0980 chunk 297 optimal weight: 20.0000 chunk 444 optimal weight: 0.0030 chunk 470 optimal weight: 0.0050 chunk 232 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 overall best weight: 1.0208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN D 179 ASN E 112 GLN ** c 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44839 Z= 0.148 Angle : 0.509 10.720 61888 Z= 0.273 Chirality : 0.039 0.275 6955 Planarity : 0.004 0.066 6891 Dihedral : 21.235 177.006 8585 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 1.38 % Allowed : 9.12 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.13), residues: 4589 helix: 1.79 (0.12), residues: 1859 sheet: -0.38 (0.20), residues: 648 loop : -0.15 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 192 HIS 0.010 0.001 HIS D 138 PHE 0.017 0.001 PHE K 7 TYR 0.014 0.001 TYR a 99 ARG 0.004 0.000 ARG A1243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 182 time to evaluate : 4.728 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: A 146 MET cc_start: 0.3919 (mmt) cc_final: 0.3671 (mmt) REVERT: A 253 MET cc_start: 0.4430 (tmm) cc_final: 0.3368 (mtm) REVERT: A 470 ARG cc_start: 0.8257 (mpt-90) cc_final: 0.7920 (mmt-90) REVERT: B 1082 MET cc_start: 0.7941 (tpt) cc_final: 0.7738 (tpt) REVERT: G 35 GLU cc_start: 0.4868 (mt-10) cc_final: 0.4603 (tp30) REVERT: J 48 MET cc_start: 0.8346 (mmm) cc_final: 0.7836 (mmt) outliers start: 56 outliers final: 30 residues processed: 223 average time/residue: 0.5202 time to fit residues: 199.0334 Evaluate side-chains 192 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 392 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 350 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 422 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 364 GLN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN A1261 GLN A1290 HIS A1370 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 576 ASN B 984 HIS C 64 HIS ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS E 112 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS I 90 GLN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.149 44839 Z= 0.615 Angle : 0.864 15.806 61888 Z= 0.450 Chirality : 0.049 0.298 6955 Planarity : 0.007 0.079 6891 Dihedral : 21.724 174.731 8585 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 2.05 % Allowed : 11.12 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 4589 helix: 0.70 (0.12), residues: 1842 sheet: -0.83 (0.19), residues: 648 loop : -0.63 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP J 18 HIS 0.014 0.003 HIS C 64 PHE 0.050 0.003 PHE C 178 TYR 0.027 0.003 TYR H 140 ARG 0.013 0.001 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 169 time to evaluate : 4.595 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: A 132 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7074 (tptp) REVERT: A 253 MET cc_start: 0.5071 (tmm) cc_final: 0.3787 (mtm) REVERT: A 305 MET cc_start: 0.8185 (mmt) cc_final: 0.7805 (mmt) REVERT: A 383 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7198 (pp30) REVERT: B 699 MET cc_start: 0.8270 (tpp) cc_final: 0.7692 (tpp) REVERT: D 24 ASN cc_start: 0.3244 (t0) cc_final: 0.2659 (p0) REVERT: G 22 MET cc_start: 0.5982 (mmm) cc_final: 0.5709 (mmp) REVERT: G 49 LEU cc_start: 0.3468 (OUTLIER) cc_final: 0.2895 (mt) REVERT: d 82 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5772 (t-170) REVERT: g 41 GLU cc_start: 0.2967 (OUTLIER) cc_final: 0.2439 (mt-10) outliers start: 83 outliers final: 47 residues processed: 242 average time/residue: 0.5188 time to fit residues: 215.7798 Evaluate side-chains 208 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain g residue 41 GLU Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 158 optimal weight: 9.9990 chunk 423 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 471 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 247 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 364 GLN A 518 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS D 17 GLN E 112 GLN J 52 HIS L 55 HIS c 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44839 Z= 0.179 Angle : 0.557 12.792 61888 Z= 0.297 Chirality : 0.040 0.221 6955 Planarity : 0.004 0.066 6891 Dihedral : 21.618 178.893 8585 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 1.21 % Allowed : 12.55 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 4589 helix: 1.50 (0.12), residues: 1841 sheet: -0.58 (0.20), residues: 627 loop : -0.36 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 192 HIS 0.009 0.001 HIS D 138 PHE 0.027 0.001 PHE I 110 TYR 0.033 0.001 TYR C 90 ARG 0.005 0.000 ARG B1094 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 168 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3643 (tmm) cc_final: 0.3339 (tmm) REVERT: A 122 MET cc_start: 0.5493 (mtt) cc_final: 0.4793 (mtm) REVERT: A 253 MET cc_start: 0.5175 (tmm) cc_final: 0.3974 (mtm) REVERT: A 383 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6735 (pp30) REVERT: A 550 MET cc_start: 0.7595 (mtt) cc_final: 0.7366 (mtt) REVERT: A 1439 MET cc_start: 0.7876 (ptp) cc_final: 0.7620 (ptp) REVERT: B 699 MET cc_start: 0.8166 (tpp) cc_final: 0.7837 (tpp) REVERT: B 1152 MET cc_start: 0.7603 (tpp) cc_final: 0.7307 (tpp) REVERT: D 24 ASN cc_start: 0.3137 (t0) cc_final: 0.2536 (p0) REVERT: G 22 MET cc_start: 0.5795 (mmm) cc_final: 0.5482 (mmm) REVERT: G 35 GLU cc_start: 0.3624 (OUTLIER) cc_final: 0.3203 (tp30) REVERT: b 39 ARG cc_start: 0.1772 (OUTLIER) cc_final: 0.1501 (mmp-170) REVERT: h 59 MET cc_start: 0.3983 (tmm) cc_final: 0.3714 (mtt) outliers start: 49 outliers final: 29 residues processed: 208 average time/residue: 0.5537 time to fit residues: 196.7888 Evaluate side-chains 191 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 454 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 396 optimal weight: 20.0000 chunk 263 optimal weight: 1.9990 chunk 469 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 44839 Z= 0.360 Angle : 0.661 13.189 61888 Z= 0.346 Chirality : 0.043 0.232 6955 Planarity : 0.005 0.068 6891 Dihedral : 21.619 176.426 8585 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.36 % Rotamer: Outliers : 1.70 % Allowed : 12.92 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 4589 helix: 1.19 (0.12), residues: 1856 sheet: -0.67 (0.20), residues: 628 loop : -0.47 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 956 HIS 0.007 0.001 HIS A 400 PHE 0.031 0.002 PHE C 178 TYR 0.024 0.002 TYR C 90 ARG 0.009 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 162 time to evaluate : 4.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3888 (tmm) cc_final: 0.3562 (tmm) REVERT: A 253 MET cc_start: 0.5127 (tmm) cc_final: 0.4049 (mtm) REVERT: A 383 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7022 (pp30) REVERT: A 1439 MET cc_start: 0.8008 (ptp) cc_final: 0.7737 (ptp) REVERT: B 699 MET cc_start: 0.8199 (tpp) cc_final: 0.7868 (tpp) REVERT: B 997 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6809 (pm20) REVERT: B 1152 MET cc_start: 0.7659 (tpp) cc_final: 0.7449 (mmm) REVERT: D 24 ASN cc_start: 0.3258 (t0) cc_final: 0.2579 (p0) REVERT: G 22 MET cc_start: 0.5942 (mmm) cc_final: 0.5603 (mmm) REVERT: G 35 GLU cc_start: 0.3849 (tp30) cc_final: 0.3534 (tp30) REVERT: I 13 MET cc_start: 0.6774 (tpt) cc_final: 0.6536 (mmm) REVERT: b 39 ARG cc_start: 0.1751 (OUTLIER) cc_final: 0.1483 (mmp-170) outliers start: 69 outliers final: 42 residues processed: 224 average time/residue: 0.5203 time to fit residues: 201.9932 Evaluate side-chains 204 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 5.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 290 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 280 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 368 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN C 252 GLN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 44839 Z= 0.154 Angle : 0.540 14.726 61888 Z= 0.286 Chirality : 0.039 0.223 6955 Planarity : 0.004 0.068 6891 Dihedral : 21.531 178.693 8585 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 0.89 % Allowed : 13.58 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.13), residues: 4589 helix: 1.74 (0.12), residues: 1838 sheet: -0.46 (0.20), residues: 625 loop : -0.26 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1307 HIS 0.007 0.001 HIS D 138 PHE 0.017 0.001 PHE K 71 TYR 0.022 0.001 TYR C 90 ARG 0.011 0.000 ARG f 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 4.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3637 (tmm) cc_final: 0.3255 (tmm) REVERT: A 122 MET cc_start: 0.5433 (mtt) cc_final: 0.4747 (mtm) REVERT: A 253 MET cc_start: 0.4944 (tmm) cc_final: 0.3685 (mtm) REVERT: A 535 MET cc_start: 0.7898 (ttp) cc_final: 0.7682 (ttt) REVERT: A 550 MET cc_start: 0.7328 (mtt) cc_final: 0.7041 (mtt) REVERT: A 1439 MET cc_start: 0.7926 (ptp) cc_final: 0.7701 (ptp) REVERT: B 699 MET cc_start: 0.7970 (tpp) cc_final: 0.7667 (tpp) REVERT: G 22 MET cc_start: 0.5862 (mmm) cc_final: 0.5601 (mmm) REVERT: b 39 ARG cc_start: 0.2028 (OUTLIER) cc_final: 0.1795 (mmp-170) outliers start: 36 outliers final: 21 residues processed: 201 average time/residue: 0.5142 time to fit residues: 180.1276 Evaluate side-chains 178 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 426 optimal weight: 3.9990 chunk 449 optimal weight: 30.0000 chunk 410 optimal weight: 10.0000 chunk 437 optimal weight: 20.0000 chunk 263 optimal weight: 0.4980 chunk 190 optimal weight: 10.0000 chunk 343 optimal weight: 0.2980 chunk 134 optimal weight: 10.0000 chunk 395 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 435 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN e 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 44839 Z= 0.362 Angle : 0.653 14.451 61888 Z= 0.341 Chirality : 0.042 0.189 6955 Planarity : 0.005 0.066 6891 Dihedral : 21.576 176.502 8585 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 1.16 % Allowed : 13.71 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.12), residues: 4589 helix: 1.38 (0.12), residues: 1849 sheet: -0.69 (0.20), residues: 645 loop : -0.41 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 956 HIS 0.007 0.001 HIS D 138 PHE 0.032 0.002 PHE C 178 TYR 0.023 0.002 TYR C 90 ARG 0.013 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 4.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3962 (tmm) cc_final: 0.3521 (tmm) REVERT: A 122 MET cc_start: 0.5528 (mtt) cc_final: 0.4738 (mtm) REVERT: A 132 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7049 (tptp) REVERT: A 253 MET cc_start: 0.5129 (tmm) cc_final: 0.3878 (mtt) REVERT: A 383 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6978 (pp30) REVERT: A 1439 MET cc_start: 0.8009 (ptp) cc_final: 0.7728 (ptp) REVERT: B 699 MET cc_start: 0.8075 (tpp) cc_final: 0.7769 (tpp) REVERT: G 22 MET cc_start: 0.6018 (mmm) cc_final: 0.5550 (mmm) REVERT: I 77 GLU cc_start: 0.6887 (tp30) cc_final: 0.6654 (tm-30) REVERT: b 39 ARG cc_start: 0.1468 (OUTLIER) cc_final: 0.1141 (mmp-170) outliers start: 47 outliers final: 36 residues processed: 197 average time/residue: 0.5087 time to fit residues: 176.0991 Evaluate side-chains 194 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 287 optimal weight: 5.9990 chunk 462 optimal weight: 5.9990 chunk 282 optimal weight: 30.0000 chunk 219 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 485 optimal weight: 0.0980 chunk 446 optimal weight: 9.9990 chunk 386 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN C 252 GLN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44839 Z= 0.207 Angle : 0.569 15.783 61888 Z= 0.301 Chirality : 0.040 0.167 6955 Planarity : 0.004 0.067 6891 Dihedral : 21.571 178.162 8585 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 0.99 % Allowed : 13.91 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4589 helix: 1.62 (0.12), residues: 1844 sheet: -0.53 (0.20), residues: 632 loop : -0.30 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 192 HIS 0.007 0.001 HIS D 138 PHE 0.017 0.001 PHE K 7 TYR 0.037 0.001 TYR B 931 ARG 0.005 0.000 ARG B1094 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3849 (tmm) cc_final: 0.3442 (tmm) REVERT: A 122 MET cc_start: 0.5302 (mtt) cc_final: 0.4602 (mtm) REVERT: A 253 MET cc_start: 0.5194 (tmm) cc_final: 0.3801 (mtm) REVERT: A 383 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6843 (pp30) REVERT: A 770 MET cc_start: 0.7383 (tpp) cc_final: 0.6508 (tpt) REVERT: A 1439 MET cc_start: 0.7885 (ptp) cc_final: 0.7638 (ptp) REVERT: B 699 MET cc_start: 0.8002 (tpp) cc_final: 0.7700 (tpp) REVERT: E 57 MET cc_start: 0.6233 (mmm) cc_final: 0.5694 (tpt) REVERT: G 22 MET cc_start: 0.5932 (mmm) cc_final: 0.5528 (mmp) REVERT: I 81 ARG cc_start: 0.4496 (tpt170) cc_final: 0.2827 (tmm160) REVERT: b 39 ARG cc_start: 0.1475 (OUTLIER) cc_final: 0.1261 (mmp-170) outliers start: 40 outliers final: 30 residues processed: 192 average time/residue: 0.5147 time to fit residues: 172.8827 Evaluate side-chains 189 residues out of total 4056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 306 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 118 optimal weight: 0.0670 chunk 356 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 386 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 397 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 overall best weight: 5.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.073244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.057127 restraints weight = 296778.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.055916 restraints weight = 246292.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.056067 restraints weight = 226366.084| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 44839 Z= 0.416 Angle : 0.732 17.301 61888 Z= 0.381 Chirality : 0.044 0.202 6955 Planarity : 0.005 0.068 6891 Dihedral : 21.789 177.137 8585 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 1.41 % Allowed : 13.56 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 4589 helix: 1.11 (0.12), residues: 1844 sheet: -0.80 (0.19), residues: 645 loop : -0.63 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1307 HIS 0.008 0.002 HIS A 817 PHE 0.036 0.002 PHE C 178 TYR 0.023 0.002 TYR C 90 ARG 0.007 0.001 ARG B 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6631.86 seconds wall clock time: 121 minutes 54.75 seconds (7314.75 seconds total)