Starting phenix.real_space_refine on Thu Jul 25 02:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/07_2024/8hpo_34935_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/07_2024/8hpo_34935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/07_2024/8hpo_34935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/07_2024/8hpo_34935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/07_2024/8hpo_34935_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/07_2024/8hpo_34935_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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 K 4 8.98 5 Zn 2 6.06 5 P 10 5.49 5 S 111 5.16 5 C 17688 2.51 5 N 4845 2.21 5 O 5291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 18": "NH1" <-> "NH2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 302": "OD1" <-> "OD2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F ASP 108": "OD1" <-> "OD2" Residue "F TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F ASP 335": "OD1" <-> "OD2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 186": "OD1" <-> "OD2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 220": "OE1" <-> "OE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 252": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 335": "OD1" <-> "OD2" Residue "G ASP 337": "OD1" <-> "OD2" Residue "G TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 367": "OE1" <-> "OE2" Residue "G TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 154": "OD1" <-> "OD2" Residue "I ASP 161": "OD1" <-> "OD2" Residue "I PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 171": "OD1" <-> "OD2" Residue "I GLU 177": "OE1" <-> "OE2" Residue "I PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 642": "OD1" <-> "OD2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 700": "OD1" <-> "OD2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ASP 707": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 818": "OD1" <-> "OD2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A ASP 881": "OD1" <-> "OD2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A ARG 906": "NH1" <-> "NH2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1012": "OD1" <-> "OD2" Residue "A TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1027": "OE1" <-> "OE2" Residue "A TYR 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1042": "OE1" <-> "OE2" Residue "A GLU 1062": "OE1" <-> "OE2" Residue "A ASP 1067": "OD1" <-> "OD2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1185": "OD1" <-> "OD2" Residue "A GLU 1193": "OE1" <-> "OE2" Residue "A PHE 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1218": "OD1" <-> "OD2" Residue "A PHE 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A GLU 1226": "OE1" <-> "OE2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1272": "OD1" <-> "OD2" Residue "A ASP 1282": "OD1" <-> "OD2" Residue "A TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1304": "OE1" <-> "OE2" Residue "A TYR 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1321": "OD1" <-> "OD2" Residue "A GLU 1326": "OE1" <-> "OE2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A TYR 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H ASP 188": "OD1" <-> "OD2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 260": "NH1" <-> "NH2" Residue "H ASP 266": "OD1" <-> "OD2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 288": "OD1" <-> "OD2" Residue "H ASP 297": "OD1" <-> "OD2" Residue "H ASP 312": "OD1" <-> "OD2" Residue "H TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 333": "OE1" <-> "OE2" Residue "H ASP 338": "OD1" <-> "OD2" Residue "H TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 347": "NH1" <-> "NH2" Residue "H GLU 368": "OE1" <-> "OE2" Residue "H PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 387": "OE1" <-> "OE2" Residue "H ASP 393": "OD1" <-> "OD2" Residue "H PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 361": "NH1" <-> "NH2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "B ASP 698": "OD1" <-> "OD2" Residue "B ASP 701": "OD1" <-> "OD2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B ASP 707": "OD1" <-> "OD2" Residue "B PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 728": "OE1" <-> "OE2" Residue "B GLU 734": "OE1" <-> "OE2" Residue "B ASP 744": "OD1" <-> "OD2" Residue "B GLU 749": "OE1" <-> "OE2" Residue "B ASP 762": "OD1" <-> "OD2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B ARG 799": "NH1" <-> "NH2" Residue "B GLU 813": "OE1" <-> "OE2" Residue "B TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 839": "OE1" <-> "OE2" Residue "B PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 872": "OD1" <-> "OD2" Residue "B GLU 874": "OE1" <-> "OE2" Residue "B GLU 878": "OE1" <-> "OE2" Residue "B ASP 881": "OD1" <-> "OD2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B ARG 906": "NH1" <-> "NH2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 939": "OD1" <-> "OD2" Residue "B GLU 951": "OE1" <-> "OE2" Residue "B ASP 958": "OD1" <-> "OD2" Residue "B ASP 976": "OD1" <-> "OD2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 987": "OD1" <-> "OD2" Residue "B TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1006": "OD1" <-> "OD2" Residue "B GLU 1008": "OE1" <-> "OE2" Residue "B TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1067": "OD1" <-> "OD2" Residue "B PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1156": "OE1" <-> "OE2" Residue "B GLU 1160": "OE1" <-> "OE2" Residue "B GLU 1166": "OE1" <-> "OE2" Residue "B ASP 1197": "OD1" <-> "OD2" Residue "B PHE 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1201": "OE1" <-> "OE2" Residue "B ASP 1202": "OD1" <-> "OD2" Residue "B TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1220": "OE1" <-> "OE2" Residue "B GLU 1226": "OE1" <-> "OE2" Residue "B GLU 1264": "OE1" <-> "OE2" Residue "B PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1298": "OE1" <-> "OE2" Residue "B PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1321": "OD1" <-> "OD2" Residue "B GLU 1326": "OE1" <-> "OE2" Residue "B ASP 1330": "OD1" <-> "OD2" Residue "B GLU 1331": "OE1" <-> "OE2" Residue "B TYR 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 63": "OD1" <-> "OD2" Residue "J TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 156": "OE1" <-> "OE2" Residue "J GLU 164": "OE1" <-> "OE2" Residue "J TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 173": "OD1" <-> "OD2" Residue "J PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J ASP 225": "OD1" <-> "OD2" Residue "J GLU 227": "OE1" <-> "OE2" Residue "J GLU 229": "OE1" <-> "OE2" Residue "J GLU 251": "OE1" <-> "OE2" Residue "J TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27951 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 2038 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 367} Link IDs: {'PTRANS': 16, 'TRANS': 396} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1279 Unresolved non-hydrogen angles: 1648 Unresolved non-hydrogen dihedrals: 1072 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 25, 'TRP:plan': 7, 'ASP:plan': 21, 'PHE:plan': 20, 'GLU:plan': 32, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 652 Chain: "D" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1385 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 1 Chain: "F" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3132 Classifications: {'peptide': 392} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 372} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "I" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1104 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "A" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5283 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 617} Chain breaks: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1936 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Chain: "E" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2077 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 5129 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 17, 'TRANS': 595} Chain breaks: 3 Chain: "J" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain breaks: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 16.08, per 1000 atoms: 0.58 Number of scatterers: 27951 At special positions: 0 Unit cell: (197.834, 130.44, 252.184, 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 2 29.99 K 4 19.00 S 111 16.00 P 10 15.00 O 5291 8.00 N 4845 7.00 C 17688 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.38 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 188 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" ND1 HIS G 188 " 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 20 sheets defined 52.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'K' and resid 2 through 23 removed outlier: 3.558A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN K 10 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS K 11 " --> pdb=" O ALA K 7 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 27 Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 108 through 117 removed outlier: 3.769A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 314 removed outlier: 3.625A pdb=" N LEU K 314 " --> pdb=" O ALA K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 342 Processing helix chain 'K' and resid 373 through 381 removed outlier: 3.771A pdb=" N ILE K 381 " --> pdb=" O ILE K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 390 through 397 Processing helix chain 'K' and resid 403 through 407 Processing helix chain 'D' and resid 15 through 35 Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 61 through 141 removed outlier: 3.637A pdb=" N GLN D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 66 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 316 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 42 through 55 removed outlier: 3.936A pdb=" N ARG F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.849A pdb=" N LYS F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS F 60 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET F 61 " --> pdb=" O TYR F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 61' Processing helix chain 'F' and resid 70 through 75 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 97 through 104 Processing helix chain 'F' and resid 115 through 136 Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.706A pdb=" N LEU F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 175 " --> pdb=" O ILE F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.510A pdb=" N LYS F 230 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 262 Proline residue: F 253 - end of helix Processing helix chain 'F' and resid 287 through 300 removed outlier: 3.535A pdb=" N HIS F 291 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL F 295 " --> pdb=" O HIS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 330 removed outlier: 3.565A pdb=" N ASN F 330 " --> pdb=" O THR F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 380 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.771A pdb=" N TYR G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 55 removed outlier: 3.570A pdb=" N ARG G 46 " --> pdb=" O PRO G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 59 removed outlier: 3.500A pdb=" N LYS G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 59' Processing helix chain 'G' and resid 70 through 75 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 99 through 104 removed outlier: 3.672A pdb=" N LYS G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 136 removed outlier: 3.521A pdb=" N TYR G 119 " --> pdb=" O GLY G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 177 removed outlier: 3.612A pdb=" N LEU G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G 175 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 197 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 243 through 262 Proline residue: G 253 - end of helix Processing helix chain 'G' and resid 287 through 300 removed outlier: 4.321A pdb=" N CYS G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL G 295 " --> pdb=" O HIS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 330 removed outlier: 3.677A pdb=" N ASN G 330 " --> pdb=" O THR G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.816A pdb=" N GLY G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 380 Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 129 through 134 Processing helix chain 'I' and resid 138 through 141 removed outlier: 3.563A pdb=" N LYS I 141 " --> pdb=" O LEU I 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 142 through 149 Processing helix chain 'I' and resid 159 through 173 Processing helix chain 'I' and resid 179 through 189 removed outlier: 3.810A pdb=" N GLN I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 677 removed outlier: 3.598A pdb=" N VAL A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.553A pdb=" N TYR A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 4.440A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.575A pdb=" N PHE A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.822A pdb=" N PHE A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 802 through 839 removed outlier: 3.563A pdb=" N LEU A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.705A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 894 through 924 removed outlier: 3.876A pdb=" N GLN A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 921 " --> pdb=" O ARG A 917 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 removed outlier: 3.664A pdb=" N LEU A 928 " --> pdb=" O PHE A 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 931 through 942 removed outlier: 5.914A pdb=" N GLN A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 951 Processing helix chain 'A' and resid 982 through 997 removed outlier: 4.250A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1025 through 1039 Processing helix chain 'A' and resid 1064 through 1069 removed outlier: 3.963A pdb=" N ILE A1068 " --> pdb=" O SER A1064 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1064 through 1069' Processing helix chain 'A' and resid 1141 through 1173 removed outlier: 3.585A pdb=" N ARG A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1216 Processing helix chain 'A' and resid 1220 through 1232 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.673A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1254 removed outlier: 3.829A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1329 through 1343 Processing helix chain 'A' and resid 1362 through 1372 removed outlier: 3.605A pdb=" N PHE A1366 " --> pdb=" O ARG A1362 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A1370 " --> pdb=" O PHE A1366 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A1371 " --> pdb=" O GLY A1367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A1372 " --> pdb=" O GLN A1368 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 216 Processing helix chain 'H' and resid 230 through 295 removed outlier: 3.711A pdb=" N THR H 254 " --> pdb=" O SER H 250 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR H 287 " --> pdb=" O THR H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 Processing helix chain 'H' and resid 355 through 380 removed outlier: 3.806A pdb=" N ASP H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 403 Processing helix chain 'C' and resid 8 through 37 Proline residue: C 22 - end of helix removed outlier: 3.772A pdb=" N THR C 25 " --> pdb=" O PHE C 21 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 64 through 80 Processing helix chain 'C' and resid 81 through 114 removed outlier: 3.872A pdb=" N GLU C 85 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.517A pdb=" N HIS C 135 " --> pdb=" O MET C 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 37 Processing helix chain 'E' and resid 70 through 75 removed outlier: 3.800A pdb=" N GLU E 73 " --> pdb=" O GLN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.649A pdb=" N ILE E 87 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 189 through 218 removed outlier: 3.862A pdb=" N ALA E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU E 216 " --> pdb=" O SER E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 302 Processing helix chain 'E' and resid 318 through 374 Processing helix chain 'B' and resid 656 through 660 removed outlier: 3.820A pdb=" N ASN B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 removed outlier: 3.530A pdb=" N LYS B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 711 removed outlier: 3.548A pdb=" N TYR B 709 " --> pdb=" O LYS B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 771 through 778 removed outlier: 3.513A pdb=" N LEU B 778 " --> pdb=" O CYS B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 840 removed outlier: 3.842A pdb=" N GLU B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 806 " --> pdb=" O GLN B 802 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 872 removed outlier: 4.163A pdb=" N LYS B 864 " --> pdb=" O MET B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 883 Processing helix chain 'B' and resid 892 through 926 removed outlier: 3.631A pdb=" N LYS B 896 " --> pdb=" O PRO B 892 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 897 " --> pdb=" O VAL B 893 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 920 " --> pdb=" O TRP B 916 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 921 " --> pdb=" O ARG B 917 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 939 removed outlier: 4.069A pdb=" N LYS B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 965 removed outlier: 3.718A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.055A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 993 " --> pdb=" O LEU B 989 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 994 " --> pdb=" O CYS B 990 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 Processing helix chain 'B' and resid 1025 through 1040 Processing helix chain 'B' and resid 1064 through 1070 Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 4.510A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1189 through 1195 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1220 through 1232 removed outlier: 3.619A pdb=" N PHE B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1233 through 1240 removed outlier: 3.907A pdb=" N ALA B1236 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B1237 " --> pdb=" O ASN B1234 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS B1238 " --> pdb=" O LYS B1235 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1247 Processing helix chain 'B' and resid 1248 through 1257 removed outlier: 3.637A pdb=" N HIS B1252 " --> pdb=" O SER B1248 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B1253 " --> pdb=" O LEU B1249 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS B1254 " --> pdb=" O VAL B1250 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1274 Processing helix chain 'B' and resid 1279 through 1292 Processing helix chain 'B' and resid 1330 through 1343 removed outlier: 3.680A pdb=" N LEU B1343 " --> pdb=" O THR B1339 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 80 Processing helix chain 'J' and resid 104 through 108 removed outlier: 4.476A pdb=" N SER J 108 " --> pdb=" O THR J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 135 removed outlier: 3.674A pdb=" N ASN J 134 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 153 removed outlier: 3.879A pdb=" N ILE J 148 " --> pdb=" O THR J 144 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN J 153 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 162 Processing helix chain 'J' and resid 176 through 184 Processing sheet with id=AA1, first strand: chain 'K' and resid 28 through 34 removed outlier: 3.617A pdb=" N HIS K 30 " --> pdb=" O LYS K 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 50 through 54 removed outlier: 3.708A pdb=" N SER K 51 " --> pdb=" O SER K 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 50 through 54 removed outlier: 3.708A pdb=" N SER K 51 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP K 123 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 130 through 134 removed outlier: 7.309A pdb=" N PHE K 157 " --> pdb=" O LYS K 144 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE K 146 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA K 155 " --> pdb=" O ILE K 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 190 through 192 removed outlier: 3.619A pdb=" N THR K 213 " --> pdb=" O LYS K 203 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE K 230 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP K 218 " --> pdb=" O VAL K 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL K 226 " --> pdb=" O ASP K 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 238 through 243 removed outlier: 3.735A pdb=" N GLU K 240 " --> pdb=" O CYS K 252 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS K 242 " --> pdb=" O ALA K 250 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER K 253 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE K 257 " --> pdb=" O SER K 253 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP K 271 " --> pdb=" O PHE K 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 281 through 286 removed outlier: 3.851A pdb=" N CYS K 283 " --> pdb=" O GLY K 297 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR K 298 " --> pdb=" O ALA K 302 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA K 302 " --> pdb=" O THR K 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 346 through 349 removed outlier: 3.630A pdb=" N LYS K 346 " --> pdb=" O ILE K 360 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL K 366 " --> pdb=" O TYR K 401 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR K 401 " --> pdb=" O VAL K 366 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS K 368 " --> pdb=" O ALA K 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 62 through 64 removed outlier: 7.168A pdb=" N VAL F 21 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR F 64 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR F 23 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL F 267 " --> pdb=" O MET F 306 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL F 308 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU F 269 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 181 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN F 270 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE F 183 " --> pdb=" O GLN F 270 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL F 234 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR F 205 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL F 236 " --> pdb=" O THR F 205 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER F 207 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU F 238 " --> pdb=" O SER F 207 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS F 209 " --> pdb=" O LEU F 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 61 through 64 removed outlier: 6.916A pdb=" N VAL G 21 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR G 64 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR G 23 " --> pdb=" O TYR G 64 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA G 22 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA G 142 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 267 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL G 308 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU G 269 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU G 181 " --> pdb=" O VAL G 268 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN G 270 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE G 183 " --> pdb=" O GLN G 270 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL G 234 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR G 205 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL G 236 " --> pdb=" O THR G 205 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER G 207 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU G 238 " --> pdb=" O SER G 207 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS G 209 " --> pdb=" O LEU G 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 127 Processing sheet with id=AB3, first strand: chain 'A' and resid 750 through 751 removed outlier: 3.541A pdb=" N TYR A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 975 through 977 removed outlier: 3.795A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 90 through 93 Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 735 removed outlier: 7.406A pdb=" N GLU B 734 " --> pdb=" O SER J 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 755 through 757 Processing sheet with id=AB8, first strand: chain 'B' and resid 975 through 977 removed outlier: 3.556A pdb=" N MET B1300 " --> pdb=" O ILE B1317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 86 through 91 removed outlier: 6.798A pdb=" N ILE J 138 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY J 88 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP J 225 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE J 272 " --> pdb=" O ASP J 225 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU J 227 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE J 270 " --> pdb=" O GLU J 227 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU J 229 " --> pdb=" O TYR J 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 86 through 91 removed outlier: 6.798A pdb=" N ILE J 138 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY J 88 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP J 225 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE J 272 " --> pdb=" O ASP J 225 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU J 227 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE J 270 " --> pdb=" O GLU J 227 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU J 229 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR J 213 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLN J 274 " --> pdb=" O THR J 213 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 243 through 244 1384 hydrogen bonds defined for protein. 4026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.68 Time building geometry restraints manager: 12.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 7 1.17 - 1.33: 7550 1.33 - 1.49: 9068 1.49 - 1.65: 11701 1.65 - 1.81: 181 Bond restraints: 28507 Sorted by residual: bond pdb=" N PRO F 10 " pdb=" CA PRO F 10 " ideal model delta sigma weight residual 1.467 1.690 -0.223 1.17e-02 7.31e+03 3.64e+02 bond pdb=" C LYS F 14 " pdb=" N PRO F 15 " ideal model delta sigma weight residual 1.332 1.497 -0.165 8.90e-03 1.26e+04 3.42e+02 bond pdb=" OG1 TPO E 167 " pdb=" P TPO E 167 " ideal model delta sigma weight residual 1.717 1.438 0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C PRO J 123 " pdb=" N PRO J 124 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.18e-02 7.18e+03 1.80e+02 bond pdb=" C PRO D 294 " pdb=" N PRO D 295 " ideal model delta sigma weight residual 1.332 1.502 -0.170 1.32e-02 5.74e+03 1.67e+02 ... (remaining 28502 not shown) Histogram of bond angle deviations from ideal: 87.88 - 98.04: 7 98.04 - 108.20: 1200 108.20 - 118.35: 20732 118.35 - 128.51: 16460 128.51 - 138.67: 189 Bond angle restraints: 38588 Sorted by residual: angle pdb=" C ASP F 9 " pdb=" N PRO F 10 " pdb=" CA PRO F 10 " ideal model delta sigma weight residual 119.93 138.67 -18.74 1.07e+00 8.73e-01 3.07e+02 angle pdb=" C ASP D 307 " pdb=" CA ASP D 307 " pdb=" CB ASP D 307 " ideal model delta sigma weight residual 110.79 87.91 22.88 1.66e+00 3.63e-01 1.90e+02 angle pdb=" C PRO J 123 " pdb=" N PRO J 124 " pdb=" CA PRO J 124 " ideal model delta sigma weight residual 120.38 133.86 -13.48 1.03e+00 9.43e-01 1.71e+02 angle pdb=" C PRO D 294 " pdb=" N PRO D 295 " pdb=" CA PRO D 295 " ideal model delta sigma weight residual 119.76 130.88 -11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C TPO E 167 " pdb=" CA TPO E 167 " pdb=" CB TPO E 167 " ideal model delta sigma weight residual 109.10 87.88 21.22 2.20e+00 2.07e-01 9.30e+01 ... (remaining 38583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14471 18.05 - 36.11: 1895 36.11 - 54.16: 637 54.16 - 72.21: 149 72.21 - 90.27: 55 Dihedral angle restraints: 17207 sinusoidal: 6703 harmonic: 10504 Sorted by residual: dihedral pdb=" CA GLU H 342 " pdb=" C GLU H 342 " pdb=" N SER H 343 " pdb=" CA SER H 343 " ideal model delta harmonic sigma weight residual -180.00 -127.56 -52.44 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" C ASP D 307 " pdb=" N ASP D 307 " pdb=" CA ASP D 307 " pdb=" CB ASP D 307 " ideal model delta harmonic sigma weight residual -122.60 -96.67 -25.93 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" CA LYS H 314 " pdb=" C LYS H 314 " pdb=" N THR H 315 " pdb=" CA THR H 315 " ideal model delta harmonic sigma weight residual -180.00 -131.23 -48.77 0 5.00e+00 4.00e-02 9.51e+01 ... (remaining 17204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4206 0.150 - 0.300: 41 0.300 - 0.450: 12 0.450 - 0.600: 2 0.600 - 0.749: 2 Chirality restraints: 4263 Sorted by residual: chirality pdb=" CA SEP D 309 " pdb=" N SEP D 309 " pdb=" C SEP D 309 " pdb=" CB SEP D 309 " both_signs ideal model delta sigma weight residual False 2.50 1.75 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CA TPO F 501 " pdb=" N TPO F 501 " pdb=" C TPO F 501 " pdb=" CB TPO F 501 " both_signs ideal model delta sigma weight residual False 2.53 1.88 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA LYS F 14 " pdb=" N LYS F 14 " pdb=" C LYS F 14 " pdb=" CB LYS F 14 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 4260 not shown) Planarity restraints: 5006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SEP I 174 " 0.088 2.00e-02 2.50e+03 1.78e-01 3.17e+02 pdb=" C SEP I 174 " -0.306 2.00e-02 2.50e+03 pdb=" O SEP I 174 " 0.136 2.00e-02 2.50e+03 pdb=" N ILE I 175 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP F 265 " 0.078 2.00e-02 2.50e+03 1.65e-01 2.73e+02 pdb=" C SEP F 265 " -0.284 2.00e-02 2.50e+03 pdb=" O SEP F 265 " 0.130 2.00e-02 2.50e+03 pdb=" N ALA F 266 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 165 " -0.027 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C ILE E 165 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE E 165 " -0.038 2.00e-02 2.50e+03 pdb=" N LEU E 166 " -0.033 2.00e-02 2.50e+03 ... (remaining 5003 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.10: 14 2.10 - 2.86: 10373 2.86 - 3.62: 44853 3.62 - 4.38: 77964 4.38 - 5.14: 132570 Nonbonded interactions: 265774 Sorted by model distance: nonbonded pdb=" OE2 GLU D 306 " pdb=" CD2 LEU D 324 " model vdw 1.346 3.460 nonbonded pdb=" N VAL F 2 " pdb=" OD1 ASP F 370 " model vdw 1.416 2.520 nonbonded pdb=" OD1 ASP F 184 " pdb=" K K F 503 " model vdw 1.784 2.850 nonbonded pdb=" OD2 ASP F 186 " pdb="ZN ZN F 502 " model vdw 1.809 2.230 nonbonded pdb=" O GLU I 177 " pdb=" N ASP I 179 " model vdw 1.817 2.520 ... (remaining 265769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 637 or resid 660 through 1041 or resid 1063 through 1177 o \ r resid 1187 through 1343)) selection = (chain 'B' and (resid 647 or resid 660 through 1069 or resid 1132 through 1343)) \ } ncs_group { reference = (chain 'F' and (resid 2 through 5 or resid 7 through 11 or resid 13 through 264 \ or resid 266 through 364 or resid 366 through 386 or resid 502 through 504)) selection = (chain 'G' and (resid 2 through 5 or resid 7 through 11 or resid 13 through 264 \ or resid 266 through 364 or resid 366 through 386 or resid 501 through 503)) } 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: 3.420 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: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 81.070 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.130 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.008 0.279 28507 Z= 0.472 Angle : 0.978 22.885 38588 Z= 0.573 Chirality : 0.057 0.749 4263 Planarity : 0.007 0.178 5006 Dihedral : 19.273 90.267 10403 Min Nonbonded Distance : 1.346 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.40 % Favored : 93.17 % Rotamer: Outliers : 11.26 % Allowed : 25.32 % Favored : 63.42 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.11), residues: 3487 helix: -2.11 (0.10), residues: 1728 sheet: -1.64 (0.23), residues: 389 loop : -3.20 (0.14), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 719 HIS 0.017 0.002 HIS I 173 PHE 0.024 0.002 PHE F 8 TYR 0.040 0.002 TYR E 373 ARG 0.010 0.001 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 343 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 47 MET cc_start: 0.7856 (mtp) cc_final: 0.7450 (mtp) REVERT: F 280 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7482 (ptm160) REVERT: F 380 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7898 (tp) REVERT: G 72 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7390 (tp-100) REVERT: G 99 ARG cc_start: 0.6892 (tpm170) cc_final: 0.6475 (tpm170) REVERT: G 108 ASP cc_start: 0.6946 (m-30) cc_final: 0.6622 (m-30) REVERT: G 384 LYS cc_start: 0.6710 (mmtt) cc_final: 0.6451 (mmtt) REVERT: I 95 LEU cc_start: 0.8366 (mt) cc_final: 0.7914 (mp) REVERT: A 727 GLN cc_start: 0.6823 (pp30) cc_final: 0.6576 (pp30) REVERT: A 801 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7027 (m-40) REVERT: A 872 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7494 (t0) REVERT: A 1062 GLU cc_start: 0.2107 (OUTLIER) cc_final: 0.1177 (tp30) REVERT: A 1257 MET cc_start: 0.7283 (ptp) cc_final: 0.7057 (mtp) REVERT: A 1345 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6634 (m90) REVERT: H 248 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6443 (tp30) REVERT: H 259 THR cc_start: 0.8176 (t) cc_final: 0.7965 (m) REVERT: H 313 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7434 (t0) REVERT: H 345 GLU cc_start: 0.6315 (tt0) cc_final: 0.6072 (pt0) REVERT: C 21 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7890 (t80) REVERT: C 27 ARG cc_start: 0.6582 (mtp-110) cc_final: 0.6343 (mtm110) REVERT: C 43 MET cc_start: 0.6366 (ttp) cc_final: 0.6098 (ttm) REVERT: C 49 ARG cc_start: 0.7605 (mmt90) cc_final: 0.7360 (mmt180) REVERT: C 55 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6866 (mmmt) REVERT: C 76 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: E 42 GLN cc_start: 0.5195 (OUTLIER) cc_final: 0.4952 (pt0) REVERT: B 918 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: B 1223 TRP cc_start: 0.8045 (m100) cc_final: 0.7831 (m100) REVERT: B 1225 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 1291 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7410 (tmm160) REVERT: J 110 ARG cc_start: 0.5301 (OUTLIER) cc_final: 0.5043 (tpm170) REVERT: J 149 GLN cc_start: 0.8319 (tp40) cc_final: 0.8044 (mm-40) REVERT: J 227 GLU cc_start: 0.5709 (mm-30) cc_final: 0.5291 (mm-30) REVERT: J 229 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6986 (mt-10) outliers start: 321 outliers final: 170 residues processed: 636 average time/residue: 1.3163 time to fit residues: 980.3645 Evaluate side-chains 455 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 271 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 264 PRO Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 280 ARG Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 98 LYS Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 823 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain A residue 868 ARG Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1233 ASN Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1345 HIS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 245 GLN Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 251 CYS Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1004 ASN Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1143 ASN Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1211 SER Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 265 TYR Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 148 optimal weight: 0.0070 chunk 91 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 319 optimal weight: 0.4980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 ASN D 141 HIS F 72 GLN F 105 ASN F 341 ASN F 392 ASN G 38 HIS ** G 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 ASN I 76 GLN I 82 ASN I 92 HIS I 100 HIS ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A 829 GLN A 930 HIS A 947 GLN A 959 GLN A 983 ASN A1036 HIS A1173 ASN A1293 HIS A1345 HIS H 195 GLN ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 HIS H 402 GLN E 24 ASN E 89 GLN E 192 ASN E 238 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN B 965 HIS B 998 HIS B1070 HIS B1163 GLN B1206 GLN B1216 ASN B1233 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 GLN J 237 GLN ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28507 Z= 0.189 Angle : 0.639 11.267 38588 Z= 0.333 Chirality : 0.044 0.348 4263 Planarity : 0.005 0.084 5006 Dihedral : 10.554 97.707 4241 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.53 % Favored : 94.32 % Rotamer: Outliers : 7.86 % Allowed : 27.22 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % 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: -1.79 (0.13), residues: 3487 helix: -0.25 (0.12), residues: 1741 sheet: -1.11 (0.24), residues: 384 loop : -2.42 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 403 HIS 0.009 0.001 HIS B1036 PHE 0.016 0.001 PHE A1180 TYR 0.017 0.001 TYR D 29 ARG 0.008 0.000 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 336 time to evaluate : 3.242 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: D 51 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7726 (tp) REVERT: D 54 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7342 (mt) REVERT: F 47 MET cc_start: 0.8043 (mtp) cc_final: 0.7623 (mtp) REVERT: F 179 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7614 (mtm-85) REVERT: F 345 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.4968 (mm-30) REVERT: G 72 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7256 (tp-100) REVERT: G 99 ARG cc_start: 0.6891 (tpm170) cc_final: 0.6589 (tpm170) REVERT: G 105 ASN cc_start: 0.8394 (t0) cc_final: 0.7855 (t0) REVERT: G 108 ASP cc_start: 0.6709 (m-30) cc_final: 0.6410 (m-30) REVERT: G 325 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6465 (tp30) REVERT: G 375 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7433 (p0) REVERT: I 80 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8158 (mp) REVERT: I 103 ASP cc_start: 0.7059 (t0) cc_final: 0.6647 (t0) REVERT: I 117 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7300 (t0) REVERT: A 727 GLN cc_start: 0.6917 (pp30) cc_final: 0.6667 (pp30) REVERT: A 801 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6162 (m110) REVERT: A 860 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7603 (mtm) REVERT: A 1062 GLU cc_start: 0.1977 (OUTLIER) cc_final: 0.0949 (tp30) REVERT: A 1063 MET cc_start: 0.2948 (tpt) cc_final: 0.2501 (tpt) REVERT: A 1202 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6053 (t70) REVERT: H 214 MET cc_start: 0.4597 (OUTLIER) cc_final: 0.4372 (ttt) REVERT: H 244 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.5594 (tmm-80) REVERT: H 245 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6186 (tm-30) REVERT: H 259 THR cc_start: 0.8177 (t) cc_final: 0.7967 (m) REVERT: H 313 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7323 (t0) REVERT: C 21 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7916 (t80) REVERT: C 55 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6920 (mmmt) REVERT: C 67 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.6089 (ptp90) REVERT: C 76 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: E 329 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: E 371 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7365 (ttm-80) REVERT: B 734 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6429 (pp20) REVERT: B 834 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7301 (OUTLIER) REVERT: B 1067 ASP cc_start: 0.6945 (m-30) cc_final: 0.6598 (p0) REVERT: B 1131 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5946 (tp-100) REVERT: B 1175 ARG cc_start: 0.5644 (ptp-110) cc_final: 0.4843 (mtm-85) REVERT: B 1194 MET cc_start: 0.6605 (mtm) cc_final: 0.6144 (mtm) REVERT: J 64 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6404 (pp) REVERT: J 73 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8018 (mm) REVERT: J 149 GLN cc_start: 0.8231 (tp40) cc_final: 0.7982 (mm-40) outliers start: 224 outliers final: 94 residues processed: 525 average time/residue: 1.2421 time to fit residues: 767.6093 Evaluate side-chains 387 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 269 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1233 ASN Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 245 GLN Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1004 ASN Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1131 GLN Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1319 LEU Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1323 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 265 TYR Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 320 optimal weight: 3.9990 chunk 345 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 317 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 HIS F 72 GLN G 177 HIS G 330 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 128 HIS E 192 ASN ** B1036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS J 79 HIS J 183 HIS ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28507 Z= 0.251 Angle : 0.649 13.735 38588 Z= 0.336 Chirality : 0.044 0.190 4263 Planarity : 0.005 0.084 5006 Dihedral : 9.166 87.909 4056 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.85 % Favored : 93.92 % Rotamer: Outliers : 8.21 % Allowed : 27.60 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % 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: -1.18 (0.14), residues: 3487 helix: 0.27 (0.12), residues: 1757 sheet: -0.82 (0.25), residues: 374 loop : -2.16 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 403 HIS 0.020 0.001 HIS H 220 PHE 0.021 0.002 PHE D 95 TYR 0.023 0.002 TYR B 682 ARG 0.006 0.001 ARG B1291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 287 time to evaluate : 3.239 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: D 113 CYS cc_start: 0.5446 (OUTLIER) cc_final: 0.4930 (t) REVERT: F 47 MET cc_start: 0.8002 (mtp) cc_final: 0.7679 (mtp) REVERT: F 345 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5364 (mm-30) REVERT: G 72 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7292 (tp-100) REVERT: G 99 ARG cc_start: 0.6896 (tpm170) cc_final: 0.6518 (tpm170) REVERT: G 105 ASN cc_start: 0.8374 (t0) cc_final: 0.7857 (t0) REVERT: G 204 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6764 (ttp) REVERT: G 240 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: G 325 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6402 (tp30) REVERT: I 117 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7413 (t0) REVERT: I 138 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8202 (tm) REVERT: A 727 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6716 (pp30) REVERT: A 735 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7674 (p0) REVERT: A 801 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6422 (m-40) REVERT: A 920 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: A 1062 GLU cc_start: 0.2121 (OUTLIER) cc_final: 0.1845 (tt0) REVERT: A 1063 MET cc_start: 0.2733 (tpt) cc_final: 0.0477 (pmm) REVERT: A 1202 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6108 (t70) REVERT: H 244 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.5968 (tmm-80) REVERT: H 245 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6058 (tm-30) REVERT: H 259 THR cc_start: 0.8189 (t) cc_final: 0.7924 (m) REVERT: H 313 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7348 (t0) REVERT: C 21 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7868 (t80) REVERT: C 55 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6888 (mmmt) REVERT: C 77 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: C 110 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7746 (t) REVERT: E 189 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6934 (mp) REVERT: B 648 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7101 (t) REVERT: B 674 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6879 (mmp80) REVERT: B 773 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5668 (tpp) REVERT: B 834 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7471 (mt) REVERT: B 884 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7046 (m170) REVERT: B 918 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: B 1175 ARG cc_start: 0.5505 (ptp-110) cc_final: 0.4808 (ttp-110) REVERT: B 1301 PHE cc_start: 0.5419 (OUTLIER) cc_final: 0.4821 (m-80) REVERT: J 73 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8009 (mm) REVERT: J 149 GLN cc_start: 0.8170 (tp40) cc_final: 0.7898 (mm-40) REVERT: J 255 GLU cc_start: 0.6521 (pp20) cc_final: 0.6298 (pp20) outliers start: 234 outliers final: 116 residues processed: 476 average time/residue: 1.2239 time to fit residues: 689.2906 Evaluate side-chains 392 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 249 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1233 ASN Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 245 GLN Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 265 TYR Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 9.9990 chunk 240 optimal weight: 0.0670 chunk 166 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 321 optimal weight: 0.4980 chunk 340 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 HIS F 72 GLN F 105 ASN ** G 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 183 HIS ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 28507 Z= 0.161 Angle : 0.575 12.640 38588 Z= 0.296 Chirality : 0.041 0.198 4263 Planarity : 0.004 0.078 5006 Dihedral : 8.224 87.754 4028 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 7.02 % Allowed : 28.73 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3487 helix: 0.87 (0.12), residues: 1759 sheet: -0.58 (0.25), residues: 373 loop : -1.89 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 719 HIS 0.016 0.001 HIS H 220 PHE 0.023 0.001 PHE A1305 TYR 0.025 0.001 TYR B 682 ARG 0.006 0.000 ARG I 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6974 Ramachandran restraints generated. 3487 Oldfield, 0 Emsley, 3487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 293 time to evaluate : 3.407 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: D 51 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7727 (tp) REVERT: D 94 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: D 291 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.4167 (tttt) REVERT: F 47 MET cc_start: 0.8046 (mtp) cc_final: 0.7695 (mtp) REVERT: F 179 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6579 (mtm180) REVERT: G 72 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7217 (tp-100) REVERT: G 105 ASN cc_start: 0.8268 (t0) cc_final: 0.7747 (t0) REVERT: G 269 LEU cc_start: 0.8659 (tt) cc_final: 0.8113 (tp) REVERT: G 325 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6537 (tp30) REVERT: G 375 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7254 (p0) REVERT: I 138 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8134 (tm) REVERT: A 727 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6735 (pp30) REVERT: A 735 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7683 (p0) REVERT: A 801 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.5930 (m110) REVERT: A 875 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7395 (mtp180) REVERT: A 1063 MET cc_start: 0.2480 (tpt) cc_final: 0.0434 (pmm) REVERT: A 1289 GLN cc_start: 0.8935 (mt0) cc_final: 0.8687 (mt0) REVERT: H 214 MET cc_start: 0.4296 (OUTLIER) cc_final: 0.4085 (ptm) REVERT: H 244 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.5399 (tmm-80) REVERT: H 259 THR cc_start: 0.8169 (t) cc_final: 0.7925 (m) REVERT: C 21 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7703 (t80) REVERT: C 55 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6997 (mmmt) REVERT: C 77 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: E 32 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7151 (ttp-170) REVERT: B 719 TRP cc_start: 0.6360 (t60) cc_final: 0.6069 (t60) REVERT: B 773 MET cc_start: 0.5894 (tpp) cc_final: 0.5499 (tpp) REVERT: B 788 TRP cc_start: 0.6824 (OUTLIER) cc_final: 0.5063 (m100) REVERT: B 834 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7132 (mt) REVERT: B 884 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6973 (m170) REVERT: B 897 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7091 (mmt-90) REVERT: B 1131 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5782 (tp-100) REVERT: B 1175 ARG cc_start: 0.5419 (ptp-110) cc_final: 0.4682 (mtm-85) REVERT: B 1187 LEU cc_start: 0.2409 (OUTLIER) cc_final: 0.1856 (pp) REVERT: B 1301 PHE cc_start: 0.5342 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: J 149 GLN cc_start: 0.8168 (tp40) cc_final: 0.7934 (mm-40) outliers start: 200 outliers final: 98 residues processed: 458 average time/residue: 1.2429 time to fit residues: 672.6667 Evaluate side-chains 373 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 252 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 55 TYR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 316 ARG Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 739 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 946 LYS Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1233 ASN Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 215 CYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 244 ARG Chi-restraints excluded: chain H residue 333 GLU Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 788 TRP Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 884 HIS Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1131 GLN Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 269 SER Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2268 > 50: distance: 40 - 66: 26.001 distance: 46 - 50: 23.231 distance: 47 - 74: 18.980 distance: 50 - 51: 27.554 distance: 51 - 52: 20.480 distance: 52 - 53: 6.232 distance: 52 - 54: 14.970 distance: 54 - 55: 14.399 distance: 55 - 56: 15.259 distance: 55 - 58: 9.497 distance: 56 - 57: 17.715 distance: 56 - 66: 11.758 distance: 58 - 59: 7.334 distance: 59 - 60: 12.775 distance: 59 - 61: 16.507 distance: 60 - 62: 23.358 distance: 61 - 63: 16.860 distance: 62 - 64: 12.059 distance: 63 - 64: 12.058 distance: 64 - 65: 34.897 distance: 66 - 67: 18.418 distance: 67 - 68: 38.771 distance: 67 - 70: 20.630 distance: 68 - 69: 19.024 distance: 68 - 74: 19.197 distance: 70 - 71: 19.660 distance: 71 - 72: 11.622 distance: 71 - 73: 19.061 distance: 74 - 75: 9.555 distance: 75 - 76: 20.443 distance: 75 - 78: 20.241 distance: 76 - 77: 4.968 distance: 76 - 82: 10.175 distance: 78 - 79: 9.526 distance: 79 - 80: 16.491 distance: 79 - 81: 11.253 distance: 82 - 83: 18.152 distance: 83 - 84: 7.450 distance: 84 - 85: 13.557 distance: 84 - 86: 6.073 distance: 86 - 87: 14.344 distance: 87 - 88: 21.020 distance: 87 - 90: 26.688 distance: 88 - 89: 34.063 distance: 88 - 92: 14.212 distance: 90 - 91: 14.607 distance: 92 - 93: 20.741 distance: 93 - 94: 19.485 distance: 93 - 96: 24.434 distance: 94 - 95: 21.525 distance: 94 - 101: 31.049 distance: 96 - 97: 25.648 distance: 97 - 98: 16.955 distance: 98 - 99: 19.767 distance: 99 - 100: 48.460 distance: 101 - 102: 12.107 distance: 102 - 103: 8.344 distance: 102 - 105: 15.722 distance: 103 - 104: 12.100 distance: 103 - 109: 16.891 distance: 105 - 106: 32.566 distance: 106 - 107: 4.697 distance: 106 - 108: 9.821 distance: 109 - 110: 32.917 distance: 110 - 111: 3.561 distance: 111 - 112: 7.955 distance: 111 - 113: 12.559 distance: 113 - 114: 17.237 distance: 114 - 115: 12.884 distance: 114 - 117: 6.672 distance: 115 - 116: 17.807 distance: 115 - 118: 23.866