Starting phenix.real_space_refine on Wed Apr 17 12:39:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh4_36253/04_2024/8jh4_36253_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh4_36253/04_2024/8jh4_36253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh4_36253/04_2024/8jh4_36253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh4_36253/04_2024/8jh4_36253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh4_36253/04_2024/8jh4_36253_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh4_36253/04_2024/8jh4_36253_neut.pdb" } resolution = 3.2 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 353 5.49 5 Mg 1 5.21 5 S 200 5.16 5 C 26872 2.51 5 N 7902 2.21 5 O 9079 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 28": "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 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 GLU 634": "OE1" <-> "OE2" 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 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 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 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 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 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 40": "NH1" <-> "NH2" Residue "e ARG 42": "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 20": "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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 44415 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 11038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11038 Classifications: {'peptide': 1400} Link IDs: {'PCIS': 3, 'PTRANS': 64, 'TRANS': 1332} Chain breaks: 5 Chain: "B" Number of atoms: 9261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9261 Classifications: {'peptide': 1161} Link IDs: {'PTRANS': 52, 'TRANS': 1108} Chain breaks: 4 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: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1741 Classifications: {'peptide': 213} Modifications used: {'COO': 1} 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: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1325 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} 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: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3415 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain breaks: 1 Chain: "P" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 3631 Classifications: {'DNA': 178} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 177} Chain: "a" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 786 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} 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: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} 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: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 703 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} 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 74.462 61.192 141.615 1.00 48.57 S ATOM 549 SG CYS A 70 77.742 60.291 142.473 1.00 37.46 S ATOM 594 SG CYS A 77 76.614 63.418 143.902 1.00 28.74 S ATOM 829 SG CYS A 107 77.127 87.874 101.981 1.00 81.51 S ATOM 851 SG CYS A 110 78.091 84.475 100.784 1.00 88.03 S ATOM 1157 SG CYS A 148 79.964 87.550 99.577 1.00107.02 S ATOM 1163 SG CYS A 168 76.314 86.987 98.413 1.00 97.61 S ATOM 19831 SG CYS B1163 86.887 63.570 129.751 1.00 26.13 S ATOM 19849 SG CYS B1166 84.855 66.761 129.177 1.00 30.15 S ATOM 19972 SG CYS B1182 83.200 63.338 129.842 1.00 42.41 S ATOM 19995 SG CYS B1185 84.894 64.179 126.502 1.00 48.09 S ATOM 20940 SG CYS C 85 85.311 70.081 209.670 1.00 95.49 S ATOM 20953 SG CYS C 87 82.698 69.461 207.633 1.00 96.30 S ATOM 20988 SG CYS C 91 82.202 70.289 210.887 1.00 89.31 S ATOM 21011 SG CYS C 94 83.834 73.259 208.891 1.00 66.65 S ATOM 29100 SG CYS I 75 76.224 164.924 156.511 1.00110.74 S ATOM 29338 SG CYS I 103 73.628 162.036 158.268 1.00100.19 S ATOM 28738 SG CYS I 29 55.556 146.835 114.879 1.00120.13 S ATOM 28763 SG CYS I 32 53.696 148.697 114.131 1.00119.31 S ATOM 29479 SG CYS J 7 84.427 104.384 201.352 1.00 20.22 S ATOM 29502 SG CYS J 10 87.204 103.603 203.877 1.00 20.22 S ATOM 29778 SG CYS J 44 87.264 106.859 201.649 1.00 20.22 S ATOM 29784 SG CYS J 45 84.978 106.201 204.703 1.00 20.22 S ATOM 30946 SG CYS L 33 45.368 87.916 188.964 1.00 71.34 S ATOM 31071 SG CYS L 50 43.084 85.113 189.306 1.00 93.28 S ATOM 31095 SG CYS L 53 41.686 88.637 188.662 1.00110.38 S Time building chain proxies: 22.60, per 1000 atoms: 0.51 Number of scatterers: 44415 At special positions: 0 Unit cell: (170.66, 181.26, 239.56, 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 353 15.00 Mg 1 11.99 O 9079 8.00 N 7902 7.00 C 26872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.43 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " 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 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " 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 87 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb=" ZN I 202 " 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 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " Number of angles added : 27 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8754 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 58 sheets defined 44.5% alpha, 16.4% beta 149 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 18.31 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: 4.123A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.803A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.504A 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: 3.606A 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 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: 3.988A 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 Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.660A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.640A pdb=" N LEU A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.797A 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: 3.591A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.698A 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 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: 4.120A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.373A 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: 3.589A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 4.063A 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 961 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: 3.969A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 3.815A pdb=" N ASP A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.554A pdb=" N ALA A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1149 Processing helix chain 'A' and resid 1168 through 1174 Processing helix chain 'A' and resid 1200 through 1207 removed outlier: 3.574A pdb=" N MET A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.584A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.738A 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 removed outlier: 3.518A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) 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: 4.067A 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 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.910A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1443 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.944A 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: 5.592A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.697A 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 removed outlier: 3.657A pdb=" N VAL B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.589A pdb=" N LYS B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.631A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.764A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.042A 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 429 removed outlier: 3.707A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.665A 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: 4.312A 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: 3.746A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.871A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.502A 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: 3.556A 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: 3.618A 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: 3.679A 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 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.933A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.529A 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 91 through 95 removed outlier: 3.535A pdb=" N SER C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) 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: 3.836A 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: 3.566A pdb=" N CYS D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.559A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.918A pdb=" N ALA D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.922A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 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: 3.501A 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 137 through 140 removed outlier: 3.691A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 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 removed outlier: 3.568A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 86 through 103 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: 3.563A 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 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: 4.149A 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: 3.526A 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: 3.718A 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 44 through 57 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: 3.500A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.594A 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: 4.357A 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 'c' and resid 112 through 116 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 24 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.501A 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 16 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.373A 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 'g' and resid 112 through 116 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 removed outlier: 3.623A pdb=" N ARG B1215 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.167A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 239 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 4.434A pdb=" N LEU A 182 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.884A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.838A 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: 4.042A 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: 3.647A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.512A 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: 3.884A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.279A 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: 6.048A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR H 56 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.791A 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: 6.916A 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: 6.784A 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: 3.953A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 6.895A 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: 3.503A pdb=" N LEU A1195 " --> pdb=" O CYS A1242 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1151 " --> pdb=" O GLU A1198 " (cutoff:3.500A) removed outlier: 6.645A 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: 5.298A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.198A 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: 3.574A pdb=" N LEU B 56 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 77 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.887A 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: 3.519A 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: 6.661A pdb=" N LEU B 249 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 228 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 247 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 230 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N MET B 245 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG B 232 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER B 243 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 234 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 241 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 540 removed outlier: 4.797A pdb=" N ARG B 625 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 540 removed outlier: 4.797A pdb=" N ARG B 625 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.526A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 5.821A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.182A 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: 5.821A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS L 60 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 954 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE L 58 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL L 29 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU L 42 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (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: 7.049A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.317A 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: 3.866A 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 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: 6.538A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.902A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 50 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.708A 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: 4.630A 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: 6.425A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE4, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.356A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE6, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.217A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.736A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR G 158 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE G 109 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 130 through 132 removed outlier: 3.956A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.831A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF6, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AF7, 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=AF7 Processing sheet with id=AF8, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AF9, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AG1, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.771A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG3, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.013A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'g' and resid 77 through 78 1741 hydrogen bonds defined for protein. 4863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 760 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 32.03 Time building geometry restraints manager: 19.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7160 1.32 - 1.45: 13287 1.45 - 1.57: 24471 1.57 - 1.70: 703 1.70 - 1.82: 326 Bond restraints: 45947 Sorted by residual: bond pdb=" CA GLY g 28 " pdb=" C GLY g 28 " ideal model delta sigma weight residual 1.516 1.468 0.048 1.12e-02 7.97e+03 1.87e+01 bond pdb=" CA MET B1210 " pdb=" C MET B1210 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.23e-02 6.61e+03 1.39e+01 bond pdb=" C GLY G 104 " pdb=" N PRO G 105 " ideal model delta sigma weight residual 1.333 1.360 -0.027 7.80e-03 1.64e+04 1.22e+01 bond pdb=" N MET B1210 " pdb=" CA MET B1210 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.19e-02 7.06e+03 1.11e+01 bond pdb=" CG MET B1210 " pdb=" SD MET B1210 " ideal model delta sigma weight residual 1.803 1.721 0.082 2.50e-02 1.60e+03 1.07e+01 ... (remaining 45942 not shown) Histogram of bond angle deviations from ideal: 98.68 - 106.10: 2943 106.10 - 113.52: 25423 113.52 - 120.94: 21631 120.94 - 128.36: 12993 128.36 - 135.78: 579 Bond angle restraints: 63569 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 113.47 106.29 7.18 1.01e+00 9.80e-01 5.06e+01 angle pdb=" N THR A1311 " pdb=" CA THR A1311 " pdb=" C THR A1311 " ideal model delta sigma weight residual 109.24 119.45 -10.21 1.51e+00 4.39e-01 4.57e+01 angle pdb=" N VAL e 117 " pdb=" CA VAL e 117 " pdb=" C VAL e 117 " ideal model delta sigma weight residual 113.47 107.58 5.89 1.01e+00 9.80e-01 3.40e+01 angle pdb=" N THR g 16 " pdb=" CA THR g 16 " pdb=" C THR g 16 " ideal model delta sigma weight residual 110.48 118.16 -7.68 1.48e+00 4.57e-01 2.70e+01 angle pdb=" C HIS h 49 " pdb=" N PRO h 50 " pdb=" CA PRO h 50 " ideal model delta sigma weight residual 119.47 125.31 -5.84 1.16e+00 7.43e-01 2.53e+01 ... (remaining 63564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 24617 28.57 - 57.13: 2258 57.13 - 85.70: 250 85.70 - 114.26: 12 114.26 - 142.83: 2 Dihedral angle restraints: 27139 sinusoidal: 13591 harmonic: 13548 Sorted by residual: dihedral pdb=" C CYS I 75 " pdb=" N CYS I 75 " pdb=" CA CYS I 75 " pdb=" CB CYS I 75 " ideal model delta harmonic sigma weight residual -122.60 -110.09 -12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C THR g 16 " pdb=" N THR g 16 " pdb=" CA THR g 16 " pdb=" CB THR g 16 " ideal model delta harmonic sigma weight residual -122.00 -132.01 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" N CYS I 75 " pdb=" C CYS I 75 " pdb=" CA CYS I 75 " pdb=" CB CYS I 75 " ideal model delta harmonic sigma weight residual 122.80 112.83 9.97 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 27136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 6710 0.092 - 0.183: 404 0.183 - 0.275: 18 0.275 - 0.367: 6 0.367 - 0.458: 1 Chirality restraints: 7139 Sorted by residual: chirality pdb=" CA THR g 16 " pdb=" N THR g 16 " pdb=" C THR g 16 " pdb=" CB THR g 16 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA CYS I 75 " pdb=" N CYS I 75 " pdb=" C CYS I 75 " pdb=" CB CYS I 75 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3' DG T 27 " pdb=" C4' DG T 27 " pdb=" O3' DG T 27 " pdb=" C2' DG T 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 7136 not shown) Planarity restraints: 6963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 80 " 0.072 2.00e-02 2.50e+03 5.36e-02 4.31e+01 pdb=" CG HIS A 80 " -0.085 2.00e-02 2.50e+03 pdb=" ND1 HIS A 80 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS A 80 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS A 80 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS A 80 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 130 " -0.034 2.00e-02 2.50e+03 4.49e-02 4.04e+01 pdb=" CG TYR G 130 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR G 130 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR G 130 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR G 130 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR G 130 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR G 130 " 0.044 2.00e-02 2.50e+03 pdb=" OH TYR G 130 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 20 " 0.075 2.00e-02 2.50e+03 4.21e-02 3.55e+01 pdb=" CG TYR H 20 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR H 20 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 20 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR H 20 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR H 20 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR H 20 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR H 20 " 0.067 2.00e-02 2.50e+03 ... (remaining 6960 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 226 2.56 - 3.15: 34073 3.15 - 3.73: 71981 3.73 - 4.32: 102099 4.32 - 4.90: 159854 Nonbonded interactions: 368233 Sorted by model distance: nonbonded pdb=" O PRO A 5 " pdb=" NH1 ARG B1159 " model vdw 1.977 2.520 nonbonded pdb=" O3' G P 10 " pdb="MG MG A1803 " model vdw 2.022 2.170 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1803 " model vdw 2.039 2.170 nonbonded pdb=" NH2 ARG D 67 " pdb=" OE2 GLU G 35 " model vdw 2.086 2.520 nonbonded pdb=" O VAL A 830 " pdb=" NZ LYS B 500 " model vdw 2.097 2.520 ... (remaining 368228 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' selection = (chain 'e' and resid 38 through 133) } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 25 through 101) } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 34 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.060 Extract box with map and model: 12.030 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 145.150 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.310 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 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 0.082 45947 Z= 0.292 Angle : 0.763 10.208 63569 Z= 0.491 Chirality : 0.046 0.458 7139 Planarity : 0.005 0.132 6963 Dihedral : 19.426 142.828 18385 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.87 % Rotamer: Outliers : 0.17 % Allowed : 1.03 % Favored : 98.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.46 % 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: -0.84 (0.12), residues: 4607 helix: 0.12 (0.11), residues: 1838 sheet: -1.15 (0.20), residues: 636 loop : -0.86 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 234 HIS 0.016 0.001 HIS C 104 PHE 0.034 0.002 PHE B 217 TYR 0.090 0.002 TYR G 130 ARG 0.011 0.001 ARG a 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 538 time to evaluate : 4.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.5348 (mpt) cc_final: 0.5113 (mtt) REVERT: B 349 LEU cc_start: 0.7853 (mm) cc_final: 0.7560 (tt) REVERT: B 730 MET cc_start: -0.0849 (ttp) cc_final: -0.1924 (ptm) REVERT: F 119 GLN cc_start: 0.6914 (mt0) cc_final: 0.6622 (mt0) outliers start: 7 outliers final: 0 residues processed: 544 average time/residue: 0.6981 time to fit residues: 584.7700 Evaluate side-chains 237 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 207 optimal weight: 0.3980 chunk 127 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 386 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 447 optimal weight: 8.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 511 GLN A 769 GLN A 974 HIS A1021 GLN ** A1393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN D 46 HIS D 170 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN G 21 GLN G 118 ASN I 90 GLN L 43 ASN c 104 GLN c 110 ASN d 84 ASN e 76 GLN e 108 ASN ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 45947 Z= 0.273 Angle : 0.622 13.645 63569 Z= 0.336 Chirality : 0.042 0.247 7139 Planarity : 0.005 0.063 6963 Dihedral : 21.828 141.130 9051 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 0.98 % Allowed : 7.53 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.13 (0.12), residues: 4607 helix: 1.09 (0.12), residues: 1862 sheet: -0.68 (0.20), residues: 647 loop : -0.48 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.007 0.001 HIS g 82 PHE 0.022 0.002 PHE a 78 TYR 0.029 0.002 TYR b 51 ARG 0.008 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 374 MET cc_start: 0.6665 (ttm) cc_final: 0.6290 (mtp) REVERT: B 730 MET cc_start: -0.1347 (ttp) cc_final: -0.1933 (ptm) REVERT: G 1 MET cc_start: 0.3878 (tmm) cc_final: 0.2741 (ptm) REVERT: a 120 MET cc_start: 0.2077 (mmt) cc_final: 0.1048 (tpt) outliers start: 40 outliers final: 21 residues processed: 284 average time/residue: 0.5857 time to fit residues: 277.7533 Evaluate side-chains 219 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain h residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 248 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 372 optimal weight: 4.9990 chunk 304 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 448 optimal weight: 30.0000 chunk 484 optimal weight: 30.0000 chunk 399 optimal weight: 20.0000 chunk 444 optimal weight: 3.9990 chunk 152 optimal weight: 0.1980 chunk 359 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 109 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS A1393 ASN B 641 ASN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN K 85 GLN L 43 ASN L 55 HIS b 25 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 45947 Z= 0.303 Angle : 0.593 9.729 63569 Z= 0.322 Chirality : 0.042 0.378 7139 Planarity : 0.005 0.052 6963 Dihedral : 21.994 138.141 9051 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 1.50 % Allowed : 9.18 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.41 (0.12), residues: 4607 helix: 1.31 (0.12), residues: 1859 sheet: -0.50 (0.20), residues: 634 loop : -0.34 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 146 HIS 0.011 0.001 HIS A 452 PHE 0.028 0.002 PHE b 61 TYR 0.028 0.002 TYR a 99 ARG 0.023 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 4.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.7493 (mtm) cc_final: 0.7119 (mtp) REVERT: A 635 MET cc_start: 0.7678 (tpt) cc_final: 0.7191 (tpt) REVERT: B 374 MET cc_start: 0.6714 (ttm) cc_final: 0.6309 (mtp) REVERT: B 730 MET cc_start: -0.1427 (ttp) cc_final: -0.1854 (tpt) REVERT: C 20 MET cc_start: 0.6438 (tmm) cc_final: 0.6006 (ttp) REVERT: D 34 PHE cc_start: 0.2343 (m-80) cc_final: 0.1276 (m-10) REVERT: D 40 ASP cc_start: 0.2965 (OUTLIER) cc_final: 0.1624 (t0) REVERT: E 34 MET cc_start: 0.7893 (mmt) cc_final: 0.7693 (mmt) REVERT: G 1 MET cc_start: 0.4358 (tmm) cc_final: 0.3553 (ptm) REVERT: G 42 PHE cc_start: 0.3634 (m-80) cc_final: 0.3423 (m-80) outliers start: 61 outliers final: 29 residues processed: 272 average time/residue: 0.5337 time to fit residues: 252.7689 Evaluate side-chains 220 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain h residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 443 optimal weight: 20.0000 chunk 337 optimal weight: 30.0000 chunk 232 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 450 optimal weight: 8.9990 chunk 476 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 426 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** A 787 HIS A 974 HIS B 317 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45947 Z= 0.172 Angle : 0.509 8.620 63569 Z= 0.278 Chirality : 0.039 0.179 7139 Planarity : 0.003 0.046 6963 Dihedral : 21.907 142.653 9051 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 1.06 % Allowed : 10.53 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.80 (0.13), residues: 4607 helix: 1.71 (0.12), residues: 1851 sheet: -0.34 (0.20), residues: 642 loop : -0.16 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 183 HIS 0.008 0.001 HIS a 113 PHE 0.018 0.001 PHE b 61 TYR 0.031 0.001 TYR h 83 ARG 0.003 0.000 ARG e 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 MET cc_start: 0.7298 (mpp) cc_final: 0.6818 (ppp) REVERT: B 374 MET cc_start: 0.6643 (ttm) cc_final: 0.6224 (mtp) REVERT: B 730 MET cc_start: -0.1587 (ttp) cc_final: -0.1892 (tpt) REVERT: B 1094 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.6893 (tpt90) REVERT: D 142 ILE cc_start: 0.4019 (mt) cc_final: 0.3207 (tt) outliers start: 43 outliers final: 23 residues processed: 249 average time/residue: 0.5525 time to fit residues: 238.2850 Evaluate side-chains 211 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 4.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain h residue 54 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 396 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 354 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 406 optimal weight: 20.0000 chunk 329 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 243 optimal weight: 0.8980 chunk 427 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- 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** A 974 HIS B 932 HIS B 996 HIS ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN I 12 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 45947 Z= 0.293 Angle : 0.553 8.645 63569 Z= 0.301 Chirality : 0.041 0.194 7139 Planarity : 0.004 0.046 6963 Dihedral : 22.006 139.846 9051 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 1.33 % Allowed : 11.39 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 4607 helix: 1.69 (0.12), residues: 1849 sheet: -0.47 (0.20), residues: 646 loop : -0.20 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 146 HIS 0.010 0.001 HIS A 452 PHE 0.020 0.002 PHE B 38 TYR 0.016 0.002 TYR E 186 ARG 0.004 0.000 ARG B 942 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 4.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 374 MET cc_start: 0.6725 (ttm) cc_final: 0.6274 (mtp) REVERT: B 730 MET cc_start: -0.1470 (ttp) cc_final: -0.1780 (tpt) REVERT: C 20 MET cc_start: 0.6605 (tmm) cc_final: 0.6064 (ttp) REVERT: D 40 ASP cc_start: 0.2883 (OUTLIER) cc_final: 0.1237 (t0) REVERT: a 120 MET cc_start: 0.2483 (mmt) cc_final: 0.1751 (tpt) outliers start: 54 outliers final: 37 residues processed: 239 average time/residue: 0.5708 time to fit residues: 238.0189 Evaluate side-chains 220 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Chi-restraints excluded: chain f residue 63 GLU Chi-restraints excluded: chain h residue 54 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 0.7980 chunk 429 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 279 optimal weight: 0.0970 chunk 117 optimal weight: 10.0000 chunk 476 optimal weight: 20.0000 chunk 395 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 157 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 overall best weight: 1.5840 ------------------------------------------------------------------------------- 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** A 974 HIS B 436 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45947 Z= 0.176 Angle : 0.497 8.416 63569 Z= 0.272 Chirality : 0.039 0.155 7139 Planarity : 0.003 0.052 6963 Dihedral : 21.967 143.160 9051 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 1.06 % Allowed : 11.93 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.93 (0.13), residues: 4607 helix: 1.85 (0.12), residues: 1856 sheet: -0.39 (0.20), residues: 652 loop : -0.09 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 192 HIS 0.011 0.001 HIS g 82 PHE 0.033 0.001 PHE b 61 TYR 0.014 0.001 TYR D 108 ARG 0.004 0.000 ARG e 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 MET cc_start: 0.7164 (mpp) cc_final: 0.6603 (ppp) REVERT: B 374 MET cc_start: 0.6694 (ttm) cc_final: 0.6259 (mtp) REVERT: B 730 MET cc_start: -0.1471 (ttp) cc_final: -0.1759 (tpt) REVERT: C 20 MET cc_start: 0.6648 (tmm) cc_final: 0.6080 (ttp) REVERT: D 142 ILE cc_start: 0.3691 (mt) cc_final: 0.2867 (tt) outliers start: 43 outliers final: 29 residues processed: 230 average time/residue: 0.5648 time to fit residues: 225.6636 Evaluate side-chains 213 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 4.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 459 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 348 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 475 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 GLN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 974 HIS ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 45947 Z= 0.234 Angle : 0.521 8.067 63569 Z= 0.283 Chirality : 0.039 0.156 7139 Planarity : 0.004 0.045 6963 Dihedral : 21.998 141.812 9051 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 1.23 % Allowed : 12.42 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.90 (0.13), residues: 4607 helix: 1.82 (0.12), residues: 1861 sheet: -0.40 (0.20), residues: 645 loop : -0.10 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 146 HIS 0.009 0.001 HIS g 82 PHE 0.028 0.001 PHE b 61 TYR 0.013 0.001 TYR D 108 ARG 0.006 0.000 ARG a 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 4.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.4767 (ttt) cc_final: 0.4328 (mtp) REVERT: A 1269 HIS cc_start: 0.6585 (OUTLIER) cc_final: 0.6154 (m170) REVERT: C 20 MET cc_start: 0.6658 (tmm) cc_final: 0.6129 (ttp) REVERT: C 21 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7156 (mt) REVERT: G 52 MET cc_start: 0.5605 (tpp) cc_final: 0.5220 (tpp) outliers start: 50 outliers final: 35 residues processed: 238 average time/residue: 0.5563 time to fit residues: 230.5355 Evaluate side-chains 217 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 4.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1269 HIS Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Chi-restraints excluded: chain g residue 74 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 293 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 302 optimal weight: 0.0670 chunk 323 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 373 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN A 649 ASN A 974 HIS D 179 ASN E 36 GLN I 12 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 45947 Z= 0.135 Angle : 0.482 9.834 63569 Z= 0.263 Chirality : 0.038 0.149 7139 Planarity : 0.003 0.045 6963 Dihedral : 21.915 144.603 9051 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 0.83 % Allowed : 13.15 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.12 (0.13), residues: 4607 helix: 2.01 (0.12), residues: 1863 sheet: -0.28 (0.20), residues: 630 loop : 0.00 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 192 HIS 0.006 0.001 HIS g 82 PHE 0.020 0.001 PHE b 61 TYR 0.032 0.001 TYR a 99 ARG 0.006 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 4.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.4778 (ttt) cc_final: 0.4414 (mtp) REVERT: B 1094 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.6709 (tpt90) REVERT: C 20 MET cc_start: 0.6701 (tmm) cc_final: 0.6143 (ttp) REVERT: C 21 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7121 (mt) REVERT: G 1 MET cc_start: 0.3832 (ptm) cc_final: 0.3618 (ptt) outliers start: 34 outliers final: 23 residues processed: 231 average time/residue: 0.5665 time to fit residues: 225.0084 Evaluate side-chains 209 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 4.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 415 optimal weight: 10.0000 chunk 442 optimal weight: 20.0000 chunk 266 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 400 optimal weight: 20.0000 chunk 418 optimal weight: 20.0000 chunk 441 optimal weight: 9.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN A 632 HIS A 649 ASN A 974 HIS ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN I 12 ASN I 22 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 45947 Z= 0.408 Angle : 0.633 10.757 63569 Z= 0.338 Chirality : 0.043 0.164 7139 Planarity : 0.005 0.060 6963 Dihedral : 22.177 139.502 9051 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 1.25 % Allowed : 13.18 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.63 (0.13), residues: 4607 helix: 1.53 (0.12), residues: 1866 sheet: -0.43 (0.20), residues: 661 loop : -0.23 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 146 HIS 0.011 0.002 HIS A 452 PHE 0.027 0.002 PHE C 178 TYR 0.028 0.002 TYR a 99 ARG 0.006 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.6773 (mpp) cc_final: 0.6294 (mtt) REVERT: A 709 MET cc_start: 0.4683 (ttt) cc_final: 0.4266 (mtp) REVERT: C 20 MET cc_start: 0.6591 (tmm) cc_final: 0.6191 (ttp) REVERT: G 1 MET cc_start: 0.4429 (ptm) cc_final: 0.4041 (ptt) outliers start: 51 outliers final: 32 residues processed: 229 average time/residue: 0.6163 time to fit residues: 245.0559 Evaluate side-chains 211 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 993 THR Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Chi-restraints excluded: chain g residue 74 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 7.9990 chunk 468 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 222 optimal weight: 0.4980 chunk 325 optimal weight: 4.9990 chunk 491 optimal weight: 7.9990 chunk 452 optimal weight: 9.9990 chunk 391 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 302 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN A 974 HIS I 12 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45947 Z= 0.192 Angle : 0.517 14.855 63569 Z= 0.281 Chirality : 0.039 0.183 7139 Planarity : 0.003 0.051 6963 Dihedral : 22.109 143.711 9051 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 0.76 % Allowed : 13.74 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.88 (0.13), residues: 4607 helix: 1.80 (0.12), residues: 1863 sheet: -0.38 (0.20), residues: 631 loop : -0.14 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 192 HIS 0.006 0.001 HIS g 82 PHE 0.018 0.001 PHE b 61 TYR 0.031 0.001 TYR a 99 ARG 0.004 0.000 ARG e 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 4.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 709 MET cc_start: 0.4723 (ttt) cc_final: 0.4343 (mtp) REVERT: A 736 MET cc_start: 0.6436 (ptp) cc_final: 0.6146 (mtm) REVERT: A 770 MET cc_start: 0.6811 (mmm) cc_final: 0.6317 (tpt) REVERT: A 1371 MET cc_start: 0.6926 (mtm) cc_final: 0.6696 (mtm) REVERT: B 1094 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.6684 (tpt90) REVERT: C 20 MET cc_start: 0.6481 (tmm) cc_final: 0.6112 (ttp) REVERT: G 1 MET cc_start: 0.4325 (ptm) cc_final: 0.3962 (ptt) outliers start: 31 outliers final: 26 residues processed: 214 average time/residue: 0.5591 time to fit residues: 207.9731 Evaluate side-chains 211 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 4.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1269 HIS Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1094 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain a residue 115 LYS Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 70 PHE Chi-restraints excluded: chain g residue 74 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 310 optimal weight: 0.3980 chunk 416 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 360 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 391 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 402 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS I 12 ASN L 43 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ---------------------------------------------------------------------------------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 45947 Z= 0.192 Angle : 0.517 13.759 63569 Z= 0.280 Chirality : 0.039 0.203 7139 Planarity : 0.003 0.048 6963 Dihedral : 22.042 143.920 9051 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 0.91 % Allowed : 13.77 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.95 (0.13), residues: 4607 helix: 1.88 (0.12), residues: 1862 sheet: -0.33 (0.20), residues: 632 loop : -0.11 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1307 HIS 0.012 0.001 HIS A 387 PHE 0.024 0.001 PHE b 61 TYR 0.029 0.001 TYR a 99 ARG 0.004 0.000 ARG e 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8564.37 seconds wall clock time: 257 minutes 27.13 seconds (15447.13 seconds total)