Starting phenix.real_space_refine on Tue Feb 20 12:54:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/02_2024/8hpo_34935_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/02_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_34935/02_2024/8hpo_34935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/02_2024/8hpo_34935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/02_2024/8hpo_34935_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpo_34935/02_2024/8hpo_34935_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27951 Number of models: 1 Model: "" Number of chains: 13 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} 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: 15.16, per 1000 atoms: 0.54 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: 10.34 Conformation dependent library (CDL) restraints added in 4.5 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... running ksdssp... Secondary structure from input PDB file: 131 helices and 17 sheets defined 46.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'K' and resid 3 through 27 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) Proline residue: K 25 - end of helix Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 108 through 116 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 341 No H-bonds generated for 'chain 'K' and resid 339 through 341' Processing helix chain 'K' and resid 372 through 380 removed outlier: 3.604A pdb=" N ALA K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 397 Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'D' and resid 15 through 34 Processing helix chain 'D' and resid 41 through 54 Processing helix chain 'D' and resid 62 through 140 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 301 through 315 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 42 through 54 Processing helix chain 'F' and resid 57 through 60 removed outlier: 3.690A pdb=" N LYS F 60 " --> pdb=" O LEU F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 57 through 60' Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.985A pdb=" N GLN F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 88 Processing helix chain 'F' and resid 94 through 103 removed outlier: 4.070A pdb=" N LYS F 98 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG F 99 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER F 101 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 135 Processing helix chain 'F' and resid 165 through 175 removed outlier: 3.623A pdb=" N ARG F 175 " --> pdb=" O ILE F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 244 through 261 Proline residue: F 253 - end of helix Processing helix chain 'F' and resid 288 through 299 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 315 through 329 Processing helix chain 'F' and resid 367 through 381 removed outlier: 4.167A pdb=" N GLU F 381 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 43 through 54 Processing helix chain 'G' and resid 57 through 59 No H-bonds generated for 'chain 'G' and resid 57 through 59' Processing helix chain 'G' and resid 71 through 77 removed outlier: 4.312A pdb=" N GLN G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 100 through 103 No H-bonds generated for 'chain 'G' and resid 100 through 103' Processing helix chain 'G' and resid 116 through 135 Processing helix chain 'G' and resid 165 through 176 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 191 through 196 Processing helix chain 'G' and resid 227 through 229 No H-bonds generated for 'chain 'G' and resid 227 through 229' Processing helix chain 'G' and resid 244 through 261 Proline residue: G 253 - end of helix Processing helix chain 'G' and resid 288 through 301 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) removed outlier: 4.328A pdb=" N PHE G 301 " --> pdb=" O TYR G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 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 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 366 through 382 removed outlier: 3.980A pdb=" N GLU G 381 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN G 382 " --> pdb=" O ALA G 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 87 Processing helix chain 'I' and resid 111 through 118 Processing helix chain 'I' and resid 130 through 133 No H-bonds generated for 'chain 'I' and resid 130 through 133' Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'I' and resid 159 through 172 Processing helix chain 'I' and resid 180 through 190 Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 699 through 710 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 714 through 724 Processing helix chain 'A' and resid 761 through 763 No H-bonds generated for 'chain 'A' and resid 761 through 763' Processing helix chain 'A' and resid 773 through 776 No H-bonds generated for 'chain 'A' and resid 773 through 776' Processing helix chain 'A' and resid 803 through 840 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) removed outlier: 4.047A pdb=" N ASN A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 847 No H-bonds generated for 'chain 'A' and resid 844 through 847' Processing helix chain 'A' and resid 862 through 870 Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 895 through 923 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 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 932 through 941 removed outlier: 5.914A pdb=" N GLN A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 952 removed outlier: 4.779A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.577A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1022 Processing helix chain 'A' and resid 1026 through 1040 Processing helix chain 'A' and resid 1065 through 1068 No H-bonds generated for 'chain 'A' and resid 1065 through 1068' Processing helix chain 'A' and resid 1142 through 1172 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 1179 through 1183 Processing helix chain 'A' and resid 1190 through 1193 No H-bonds generated for 'chain 'A' and resid 1190 through 1193' Processing helix chain 'A' and resid 1203 through 1216 Processing helix chain 'A' and resid 1221 through 1231 Processing helix chain 'A' and resid 1237 through 1239 No H-bonds generated for 'chain 'A' and resid 1237 through 1239' Processing helix chain 'A' and resid 1242 through 1255 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 1260 through 1273 Processing helix chain 'A' and resid 1281 through 1293 Processing helix chain 'A' and resid 1330 through 1342 Processing helix chain 'A' and resid 1362 through 1371 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) Processing helix chain 'H' and resid 172 through 215 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 231 through 296 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) removed outlier: 3.827A pdb=" N MET H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 341 Processing helix chain 'H' and resid 356 through 379 removed outlier: 3.806A pdb=" N ASP H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 402 Processing helix chain 'C' and resid 9 through 38 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) removed outlier: 4.335A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 54 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 81 through 113 removed outlier: 3.750A pdb=" N GLU C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS C 86 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 93 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 112 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 146 Processing helix chain 'E' and resid 23 through 36 Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 162 through 165 No H-bonds generated for 'chain 'E' and resid 162 through 165' Processing helix chain 'E' and resid 173 through 177 removed outlier: 3.920A pdb=" N ASN E 177 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 183 No H-bonds generated for 'chain 'E' and resid 181 through 183' Processing helix chain 'E' and resid 190 through 219 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 298 through 301 No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 319 through 373 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 668 through 676 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 699 through 710 removed outlier: 3.548A pdb=" N TYR B 709 " --> pdb=" O LYS B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 802 through 839 removed outlier: 3.814A pdb=" N THR B 806 " --> pdb=" O GLN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 870 Processing helix chain 'B' and resid 877 through 882 Processing helix chain 'B' and resid 893 through 927 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) removed outlier: 3.625A pdb=" N SER B 927 " --> pdb=" O VAL B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 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 945 through 964 Processing helix chain 'B' and resid 983 through 996 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 1004 through 1021 Processing helix chain 'B' and resid 1026 through 1039 Processing helix chain 'B' and resid 1065 through 1069 Processing helix chain 'B' and resid 1142 through 1163 Processing helix chain 'B' and resid 1165 through 1174 Processing helix chain 'B' and resid 1190 through 1194 Processing helix chain 'B' and resid 1203 through 1216 Processing helix chain 'B' and resid 1221 through 1231 Processing helix chain 'B' and resid 1234 through 1239 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) No H-bonds generated for 'chain 'B' and resid 1234 through 1239' Processing helix chain 'B' and resid 1242 through 1256 removed outlier: 3.682A pdb=" N LEU B1249 " --> pdb=" O VAL B1245 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B1251 " --> pdb=" O GLN B1247 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 1260 through 1273 Processing helix chain 'B' and resid 1280 through 1293 removed outlier: 4.441A pdb=" N HIS B1293 " --> pdb=" O GLN B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1342 Processing helix chain 'J' and resid 70 through 79 Processing helix chain 'J' and resid 105 through 107 No H-bonds generated for 'chain 'J' and resid 105 through 107' Processing helix chain 'J' and resid 132 through 134 No H-bonds generated for 'chain 'J' and resid 132 through 134' Processing helix chain 'J' and resid 145 through 153 removed outlier: 3.553A pdb=" N ASN J 153 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 161 No H-bonds generated for 'chain 'J' and resid 158 through 161' Processing helix chain 'J' and resid 177 through 184 Processing sheet with id= A, 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= B, first strand: chain 'K' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'K' and resid 166 through 168 removed outlier: 3.637A pdb=" N VAL K 145 " --> pdb=" O PHE K 157 " (cutoff:3.500A) Processing sheet with id= D, 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= E, first strand: chain 'K' and resid 257 through 260 removed outlier: 3.847A pdb=" N TRP K 271 " --> pdb=" O PHE K 260 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 334 through 337 removed outlier: 4.620A pdb=" N ALA K 302 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR K 298 " --> pdb=" O ALA K 302 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS K 283 " --> pdb=" O GLY K 297 " (cutoff:3.500A) Processing sheet with id= G, 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: 6.401A pdb=" N ASN K 370 " --> pdb=" O MET K 398 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N MET K 398 " --> pdb=" O ASN K 370 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 419 through 421 removed outlier: 3.617A pdb=" N HIS K 30 " --> pdb=" O LYS K 442 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 238 through 243 removed outlier: 7.097A pdb=" N CYS K 252 " --> pdb=" O GLN K 239 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE K 241 " --> pdb=" O ALA K 250 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA K 250 " --> pdb=" O ILE K 241 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 62 through 64 removed outlier: 7.152A pdb=" N MET F 305 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN F 144 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F 307 " --> pdb=" O ASN F 144 " (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) Processing sheet with id= K, 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: 6.298A pdb=" N VAL G 141 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 24 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL G 143 " --> pdb=" O PHE G 24 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET G 305 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASN G 144 " --> pdb=" O MET G 305 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL G 307 " --> pdb=" O ASN G 144 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 755 through 757 Processing sheet with id= M, 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= N, first strand: chain 'E' and resid 90 through 93 Processing sheet with id= O, first strand: chain 'B' and resid 755 through 757 Processing sheet with id= P, 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= Q, first strand: chain 'J' and resid 89 through 91 removed outlier: 8.645A pdb=" N LEU J 90 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR J 140 " --> pdb=" O LEU J 90 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU J 231 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE J 267 " --> pdb=" O LEU J 231 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU J 233 " --> pdb=" O TYR J 265 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR J 265 " --> pdb=" O LEU J 233 " (cutoff:3.500A) 1220 hydrogen bonds defined for protein. 3468 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: 9.49 Time building geometry restraints manager: 11.23 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: 10403 2.86 - 3.62: 44997 3.62 - 4.38: 78340 4.38 - 5.14: 132608 Nonbonded interactions: 266362 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 266357 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: 3.820 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: 0.030 Extract box with map and model: 15.040 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 75.710 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.140 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.870 ------------------------------------------------------------------------------- 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= 0.506 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 : 3.678 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: 1.3983 time to fit residues: 1040.1696 Evaluate side-chains 455 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 271 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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: 0.7980 chunk 148 optimal weight: 0.0070 chunk 91 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 275 optimal weight: 6.9990 chunk 106 optimal weight: 0.0570 chunk 167 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 319 optimal weight: 0.0050 overall best weight: 0.2730 ------------------------------------------------------------------------------- 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 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 690 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 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 998 HIS B1163 GLN B1206 GLN B1216 ASN B1233 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 GLN ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 237 GLN ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28507 Z= 0.176 Angle : 0.611 11.635 38588 Z= 0.319 Chirality : 0.043 0.253 4263 Planarity : 0.005 0.082 5006 Dihedral : 10.227 91.518 4241 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.88 % Favored : 94.98 % Rotamer: Outliers : 7.51 % Allowed : 27.22 % Favored : 65.28 % 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: -1.74 (0.13), residues: 3487 helix: -0.24 (0.12), residues: 1716 sheet: -1.04 (0.24), residues: 381 loop : -2.33 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 719 HIS 0.008 0.001 HIS B 998 PHE 0.016 0.001 PHE A1017 TYR 0.018 0.001 TYR D 29 ARG 0.008 0.000 ARG A 674 *********************** 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 548 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 334 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7359 (mt) REVERT: F 47 MET cc_start: 0.7737 (mtp) cc_final: 0.7354 (mtp) REVERT: F 345 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.4821 (mm-30) REVERT: G 72 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7184 (tp-100) REVERT: G 105 ASN cc_start: 0.8257 (t0) cc_final: 0.7701 (t0) REVERT: G 108 ASP cc_start: 0.6729 (m-30) cc_final: 0.6450 (m-30) REVERT: G 325 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6429 (tp30) REVERT: G 375 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7342 (p0) REVERT: I 80 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8199 (mp) REVERT: I 103 ASP cc_start: 0.7009 (t0) cc_final: 0.6657 (t0) REVERT: A 727 GLN cc_start: 0.6947 (pp30) cc_final: 0.6702 (pp30) REVERT: A 801 ASN cc_start: 0.6901 (OUTLIER) cc_final: 0.5944 (m-40) REVERT: A 1202 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6162 (t70) REVERT: H 205 LEU cc_start: 0.3162 (OUTLIER) cc_final: 0.2947 (tp) REVERT: H 245 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6224 (tm-30) REVERT: C 21 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7922 (t80) REVERT: C 55 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6946 (mmmt) REVERT: C 76 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: E 371 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7364 (ttm-80) REVERT: B 734 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6411 (pp20) REVERT: B 773 MET cc_start: 0.6007 (tpp) cc_final: 0.5741 (tpp) REVERT: B 834 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7124 (mt) REVERT: B 1067 ASP cc_start: 0.6761 (m-30) cc_final: 0.6478 (p0) REVERT: B 1131 GLN cc_start: 0.6240 (OUTLIER) cc_final: 0.5895 (tp-100) REVERT: B 1175 ARG cc_start: 0.5416 (ptp-110) cc_final: 0.4730 (ttp-110) REVERT: B 1225 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7983 (mm-30) REVERT: B 1248 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7631 (t) REVERT: J 64 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6406 (pp) REVERT: J 73 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8035 (mm) REVERT: J 149 GLN cc_start: 0.8202 (tp40) cc_final: 0.7943 (mm-40) REVERT: J 227 GLU cc_start: 0.6016 (mm-30) cc_final: 0.5491 (mm-30) outliers start: 214 outliers final: 87 residues processed: 520 average time/residue: 1.2730 time to fit residues: 778.5418 Evaluate side-chains 363 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 259 time to evaluate : 3.435 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain F residue 214 PHE 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 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 16 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 75 CYS 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 199 THR 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 305 MET Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 646 VAL 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 861 THR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 1006 ASP 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 205 LEU Chi-restraints excluded: chain H residue 208 LEU 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 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 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 42 GLN 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 286 ASP Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 371 ARG 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 857 HIS Chi-restraints excluded: chain B residue 890 THR 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 1248 SER Chi-restraints excluded: chain B residue 1319 LEU Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 111 HIS 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 272 ILE 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: 0.7980 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 345 optimal weight: 7.9990 chunk 285 optimal weight: 7.9990 chunk 317 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN F 43 HIS F 72 GLN G 177 HIS ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 GLN ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A1132 ASN ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 402 GLN C 6 ASN C 71 ASN C 128 HIS E 192 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS J 79 HIS ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28507 Z= 0.259 Angle : 0.638 13.478 38588 Z= 0.331 Chirality : 0.044 0.176 4263 Planarity : 0.005 0.083 5006 Dihedral : 8.739 87.954 4026 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Rotamer: Outliers : 7.65 % Allowed : 27.99 % Favored : 64.36 % 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: -1.31 (0.14), residues: 3487 helix: 0.08 (0.12), residues: 1737 sheet: -0.78 (0.25), residues: 374 loop : -2.10 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 403 HIS 0.019 0.001 HIS H 220 PHE 0.021 0.002 PHE D 95 TYR 0.025 0.002 TYR B 682 ARG 0.005 0.000 ARG I 160 *********************** 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 516 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 298 time to evaluate : 3.290 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: D 43 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6728 (mpt180) REVERT: D 113 CYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4923 (t) REVERT: F 47 MET cc_start: 0.7782 (mtp) cc_final: 0.7386 (mtp) REVERT: F 179 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.6868 (mtm180) REVERT: F 345 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5419 (mm-30) REVERT: G 72 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7228 (tp-100) REVERT: G 240 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: G 306 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7387 (ttt) REVERT: G 325 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6329 (tp30) REVERT: I 80 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8200 (mp) REVERT: I 138 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8297 (tm) REVERT: I 200 ARG cc_start: 0.7166 (ttm-80) cc_final: 0.6780 (ttm170) REVERT: A 727 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6711 (pp30) REVERT: A 735 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7695 (p0) REVERT: A 801 ASN cc_start: 0.7216 (OUTLIER) cc_final: 0.6651 (m-40) REVERT: A 860 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7047 (mtm) REVERT: A 951 GLU cc_start: 0.7245 (mp0) cc_final: 0.6921 (mp0) REVERT: A 1062 GLU cc_start: 0.2460 (OUTLIER) cc_final: 0.1327 (tp30) REVERT: A 1063 MET cc_start: 0.2937 (tpt) cc_final: 0.0598 (pmm) REVERT: A 1202 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6166 (t70) REVERT: H 245 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6066 (tm-30) REVERT: H 259 THR cc_start: 0.8179 (t) cc_final: 0.7910 (m) REVERT: C 21 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7946 (t80) REVERT: C 55 LYS cc_start: 0.7323 (mmtt) cc_final: 0.6839 (mmmt) REVERT: C 76 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: C 77 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: C 110 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7472 (t) REVERT: B 648 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6940 (t) REVERT: B 719 TRP cc_start: 0.6532 (t60) cc_final: 0.6079 (t60) REVERT: B 834 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7476 (mt) REVERT: B 918 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: B 939 ASP cc_start: 0.7103 (m-30) cc_final: 0.6877 (m-30) REVERT: B 1175 ARG cc_start: 0.5539 (ptp-110) cc_final: 0.4926 (ttp-110) REVERT: B 1187 LEU cc_start: 0.2654 (OUTLIER) cc_final: 0.2007 (pp) REVERT: B 1301 PHE cc_start: 0.5536 (OUTLIER) cc_final: 0.4907 (m-80) REVERT: J 73 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8015 (mm) REVERT: J 140 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7221 (p) REVERT: J 149 GLN cc_start: 0.8219 (tp40) cc_final: 0.7936 (mm-40) REVERT: J 250 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.5927 (mtt180) REVERT: J 255 GLU cc_start: 0.6617 (pp20) cc_final: 0.6368 (pp20) outliers start: 218 outliers final: 114 residues processed: 475 average time/residue: 1.3130 time to fit residues: 733.3354 Evaluate side-chains 405 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 263 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ARG 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 70 THR Chi-restraints excluded: chain F residue 90 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 250 VAL Chi-restraints excluded: chain F residue 277 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 345 GLU Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 72 GLN 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 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 249 SER Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 306 MET 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 80 ILE 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 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 687 LYS Chi-restraints excluded: chain A residue 700 ASP 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 833 THR Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 889 VAL 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 1067 ASP 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 245 GLN Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain H residue 333 GLU 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 76 TYR 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 94 LEU Chi-restraints excluded: chain C residue 105 GLU 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 191 LYS Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 286 ASP 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 656 ILE Chi-restraints excluded: chain B residue 683 THR 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 881 ASP 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 1035 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1323 THR 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 140 THR Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 250 ARG 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: 7.9990 chunk 240 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 321 optimal weight: 0.6980 chunk 340 optimal weight: 4.9990 chunk 167 optimal weight: 0.0060 chunk 304 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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** ** 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** J 79 HIS ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28507 Z= 0.173 Angle : 0.576 12.460 38588 Z= 0.298 Chirality : 0.042 0.164 4263 Planarity : 0.004 0.078 5006 Dihedral : 8.038 87.473 4007 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 7.09 % Allowed : 28.80 % Favored : 64.12 % 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: -0.78 (0.14), residues: 3487 helix: 0.53 (0.12), residues: 1747 sheet: -0.51 (0.25), residues: 372 loop : -1.88 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 403 HIS 0.009 0.001 HIS F 43 PHE 0.019 0.001 PHE A1017 TYR 0.028 0.001 TYR B 682 ARG 0.006 0.000 ARG G 222 *********************** 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 485 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 283 time to evaluate : 3.226 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: F 47 MET cc_start: 0.7711 (mtp) cc_final: 0.7322 (mtp) REVERT: F 179 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6842 (mtm180) REVERT: G 72 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7215 (tp-100) REVERT: G 105 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7570 (t0) REVERT: G 204 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6056 (ttp) REVERT: G 240 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: G 306 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7347 (ttt) REVERT: G 325 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6433 (tp30) REVERT: G 375 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7332 (p0) REVERT: I 80 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8157 (mp) REVERT: I 138 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8284 (tm) REVERT: I 149 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7426 (m) REVERT: A 735 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7696 (p0) REVERT: A 801 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6213 (m-40) REVERT: A 860 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7082 (mtm) REVERT: A 1062 GLU cc_start: 0.2417 (OUTLIER) cc_final: 0.1441 (tp30) REVERT: A 1063 MET cc_start: 0.2684 (tpt) cc_final: 0.0511 (pmm) REVERT: A 1289 GLN cc_start: 0.8874 (mt0) cc_final: 0.8492 (mt0) REVERT: H 222 GLU cc_start: 0.4659 (OUTLIER) cc_final: 0.4398 (pt0) REVERT: H 259 THR cc_start: 0.8188 (t) cc_final: 0.7950 (m) REVERT: C 21 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7810 (t80) REVERT: C 55 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6932 (mmmt) REVERT: C 76 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: C 77 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: E 32 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7160 (ttp-170) REVERT: B 719 TRP cc_start: 0.6269 (t60) cc_final: 0.5807 (t60) REVERT: B 773 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5698 (tpp) REVERT: B 834 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7353 (mt) REVERT: B 939 ASP cc_start: 0.7142 (m-30) cc_final: 0.6884 (m-30) REVERT: B 1175 ARG cc_start: 0.5465 (ptp-110) cc_final: 0.4832 (ttp-110) REVERT: B 1187 LEU cc_start: 0.2880 (OUTLIER) cc_final: 0.2281 (pp) REVERT: B 1301 PHE cc_start: 0.5474 (OUTLIER) cc_final: 0.4839 (m-80) REVERT: J 73 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8004 (mm) REVERT: J 140 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.7364 (p) REVERT: J 250 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.5967 (mtt180) outliers start: 202 outliers final: 95 residues processed: 452 average time/residue: 1.2654 time to fit residues: 675.4730 Evaluate side-chains 375 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 254 time to evaluate : 2.958 ------------------------------------------------------------------------------- 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 303 GLU 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 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 72 GLN Chi-restraints excluded: chain G residue 105 ASN 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 204 MET Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 80 ILE 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 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 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 860 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1040 VAL 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 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 222 GLU 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 54 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG 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 176 ILE Chi-restraints excluded: chain E residue 189 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 683 THR 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 890 THR Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1250 VAL 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 140 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 265 TYR 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 ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.3980 chunk 193 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 140 optimal weight: 0.0870 chunk 290 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 173 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN F 43 HIS ** 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** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 134 ASN J 153 ASN ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28507 Z= 0.189 Angle : 0.575 12.085 38588 Z= 0.296 Chirality : 0.042 0.312 4263 Planarity : 0.004 0.076 5006 Dihedral : 7.687 87.090 3991 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 7.02 % Allowed : 29.18 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % 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: -0.53 (0.14), residues: 3487 helix: 0.73 (0.13), residues: 1747 sheet: -0.38 (0.25), residues: 374 loop : -1.75 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 403 HIS 0.016 0.001 HIS H 220 PHE 0.026 0.001 PHE A1305 TYR 0.032 0.001 TYR B 682 ARG 0.007 0.000 ARG I 160 *********************** REFINEMENT MACRO_CYCLE 5 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 469 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 269 time to evaluate : 3.443 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: F 47 MET cc_start: 0.7734 (mtp) cc_final: 0.7335 (mtp) REVERT: F 179 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6869 (mtm180) REVERT: G 72 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7226 (tp-100) REVERT: G 105 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7552 (t0) REVERT: G 204 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5982 (ttp) REVERT: G 240 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: G 325 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6532 (tp30) REVERT: G 375 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7297 (p0) REVERT: I 80 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8148 (mp) REVERT: I 138 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8246 (tm) REVERT: I 149 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7447 (m) REVERT: I 196 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8442 (pttt) REVERT: A 691 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8167 (tt) REVERT: A 727 GLN cc_start: 0.6900 (pp30) cc_final: 0.6639 (pp30) REVERT: A 735 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7707 (p0) REVERT: A 801 ASN cc_start: 0.7010 (OUTLIER) cc_final: 0.6395 (m-40) REVERT: A 860 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6978 (mtm) REVERT: A 875 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7512 (mtp180) REVERT: A 1062 GLU cc_start: 0.2361 (OUTLIER) cc_final: 0.1589 (tp30) REVERT: A 1063 MET cc_start: 0.2562 (tpt) cc_final: 0.0451 (pmm) REVERT: H 259 THR cc_start: 0.8172 (t) cc_final: 0.7908 (m) REVERT: C 21 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7876 (t80) REVERT: C 55 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6967 (mmmt) REVERT: C 76 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: E 32 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7169 (ttp-170) REVERT: B 648 VAL cc_start: 0.7297 (OUTLIER) cc_final: 0.7054 (t) REVERT: B 719 TRP cc_start: 0.6271 (t60) cc_final: 0.5818 (t60) REVERT: B 773 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.5654 (tpp) REVERT: B 834 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7386 (mt) REVERT: B 897 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7195 (mmt-90) REVERT: B 939 ASP cc_start: 0.7071 (m-30) cc_final: 0.6789 (m-30) REVERT: B 1175 ARG cc_start: 0.5137 (ptp-110) cc_final: 0.4513 (ttp-110) REVERT: B 1187 LEU cc_start: 0.2648 (OUTLIER) cc_final: 0.2086 (pp) REVERT: B 1301 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.4821 (m-80) REVERT: J 73 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8024 (mm) REVERT: J 140 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7407 (p) REVERT: J 250 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.5948 (mtt180) outliers start: 200 outliers final: 115 residues processed: 441 average time/residue: 1.2652 time to fit residues: 666.2856 Evaluate side-chains 387 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 244 time to evaluate : 3.188 ------------------------------------------------------------------------------- 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 303 GLU Chi-restraints excluded: chain F residue 13 VAL 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 179 ARG 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 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 72 GLN Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 ASN 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 218 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 314 THR Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 80 ILE 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 178 THR Chi-restraints excluded: chain I residue 196 LYS 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 691 LEU Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE 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 860 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1040 VAL 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 1233 ASN Chi-restraints excluded: chain A residue 1313 SER 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 333 GLU 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 54 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 110 VAL 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 73 GLU 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 176 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 286 ASP 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 656 ILE Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain B residue 683 THR 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 857 HIS Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1035 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1250 VAL 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 63 ASP 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 140 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 250 ARG 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 272 ILE Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 0.7980 chunk 306 optimal weight: 0.4980 chunk 67 optimal weight: 0.0980 chunk 199 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 340 optimal weight: 0.4980 chunk 282 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 28 optimal weight: 50.0000 chunk 112 optimal weight: 2.9990 chunk 178 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 ASN F 43 HIS F 72 GLN ** G 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS J 153 ASN ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 28507 Z= 0.153 Angle : 0.548 10.893 38588 Z= 0.282 Chirality : 0.041 0.202 4263 Planarity : 0.004 0.075 5006 Dihedral : 7.391 88.815 3987 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 6.03 % Allowed : 30.09 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % 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: -0.23 (0.14), residues: 3487 helix: 0.96 (0.13), residues: 1748 sheet: -0.15 (0.25), residues: 373 loop : -1.62 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 261 HIS 0.009 0.001 HIS H 401 PHE 0.016 0.001 PHE A1017 TYR 0.031 0.001 TYR B 682 ARG 0.007 0.000 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 6 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 438 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 266 time to evaluate : 3.276 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: F 47 MET cc_start: 0.7665 (mtp) cc_final: 0.7270 (mtp) REVERT: F 179 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6713 (mtm180) REVERT: F 345 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5304 (mm-30) REVERT: G 72 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7211 (tp-100) REVERT: G 105 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7473 (t0) REVERT: G 204 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6030 (ttp) REVERT: G 240 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: I 80 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8214 (mp) REVERT: I 91 ASN cc_start: 0.8527 (m-40) cc_final: 0.8315 (m-40) REVERT: I 138 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8172 (tm) REVERT: I 196 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8398 (pttt) REVERT: A 727 GLN cc_start: 0.6945 (pp30) cc_final: 0.6703 (pp30) REVERT: A 860 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7058 (mtm) REVERT: A 1062 GLU cc_start: 0.1642 (OUTLIER) cc_final: 0.0806 (tp30) REVERT: A 1289 GLN cc_start: 0.8921 (mt0) cc_final: 0.8472 (mt0) REVERT: H 259 THR cc_start: 0.8133 (t) cc_final: 0.7872 (m) REVERT: C 21 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7779 (t80) REVERT: C 55 LYS cc_start: 0.7319 (mmtt) cc_final: 0.6987 (mmmt) REVERT: C 76 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: E 32 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7031 (ttp-170) REVERT: E 56 GLU cc_start: 0.6647 (mp0) cc_final: 0.6243 (mt-10) REVERT: B 648 VAL cc_start: 0.7325 (OUTLIER) cc_final: 0.7118 (t) REVERT: B 716 LEU cc_start: 0.4738 (OUTLIER) cc_final: 0.4519 (mp) REVERT: B 719 TRP cc_start: 0.6392 (t60) cc_final: 0.5930 (t60) REVERT: B 773 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5379 (tpt) REVERT: B 834 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.7119 (OUTLIER) REVERT: B 939 ASP cc_start: 0.6966 (m-30) cc_final: 0.6662 (m-30) REVERT: B 1175 ARG cc_start: 0.5132 (ptp-110) cc_final: 0.4501 (mtm-85) REVERT: B 1187 LEU cc_start: 0.2324 (OUTLIER) cc_final: 0.1781 (pp) REVERT: B 1301 PHE cc_start: 0.5373 (OUTLIER) cc_final: 0.4784 (m-80) REVERT: J 70 GLN cc_start: 0.7506 (pm20) cc_final: 0.7266 (mp10) REVERT: J 255 GLU cc_start: 0.6525 (pp20) cc_final: 0.6228 (pp20) outliers start: 172 outliers final: 91 residues processed: 413 average time/residue: 1.2507 time to fit residues: 610.8776 Evaluate side-chains 353 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 243 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 ASN 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 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 106 VAL 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 246 THR 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 20 ARG Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 105 ASN 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 204 MET Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 303 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 196 LYS 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 736 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 860 MET 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 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1040 VAL 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 1233 ASN Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 215 CYS 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 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 73 GLU 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 160 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 999 THR 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 1134 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1250 VAL 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 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 218 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 248 optimal weight: 0.0980 chunk 192 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 339 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN G 135 ASN G 231 ASN G 330 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 HIS A 884 HIS A 913 ASN A1274 ASN A1299 ASN H 224 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 HIS B1070 HIS ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28507 Z= 0.280 Angle : 0.626 9.732 38588 Z= 0.324 Chirality : 0.044 0.190 4263 Planarity : 0.005 0.076 5006 Dihedral : 7.355 89.623 3969 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.24 % Rotamer: Outliers : 6.35 % Allowed : 29.81 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % 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: -0.42 (0.14), residues: 3487 helix: 0.71 (0.12), residues: 1758 sheet: -0.11 (0.26), residues: 374 loop : -1.64 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 261 HIS 0.010 0.001 HIS H 220 PHE 0.024 0.002 PHE A1305 TYR 0.027 0.002 TYR B 682 ARG 0.010 0.001 ARG I 168 *********************** REFINEMENT MACRO_CYCLE 7 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 426 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 245 time to evaluate : 3.360 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: D 113 CYS cc_start: 0.5526 (OUTLIER) cc_final: 0.5038 (t) REVERT: F 47 MET cc_start: 0.7801 (mtp) cc_final: 0.7466 (mtp) REVERT: F 179 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6893 (mtm180) REVERT: F 345 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5812 (mm-30) REVERT: G 95 GLU cc_start: 0.7507 (mp0) cc_final: 0.7058 (pm20) REVERT: G 240 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: G 375 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7382 (p0) REVERT: I 80 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (mp) REVERT: I 106 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: I 138 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8354 (tm) REVERT: I 196 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8414 (pttt) REVERT: A 691 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8114 (tt) REVERT: A 727 GLN cc_start: 0.6933 (pp30) cc_final: 0.6694 (pp30) REVERT: A 735 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 801 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6850 (m-40) REVERT: A 860 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.6964 (mtm) REVERT: A 920 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: A 1062 GLU cc_start: 0.2005 (OUTLIER) cc_final: 0.0827 (tp30) REVERT: A 1202 ASP cc_start: 0.6337 (OUTLIER) cc_final: 0.5943 (t70) REVERT: H 259 THR cc_start: 0.8154 (t) cc_final: 0.7887 (m) REVERT: C 21 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7924 (t80) REVERT: C 55 LYS cc_start: 0.7401 (mmtt) cc_final: 0.7023 (mmmt) REVERT: C 76 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: C 110 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7534 (t) REVERT: E 32 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7221 (ttp-170) REVERT: B 648 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.7011 (t) REVERT: B 716 LEU cc_start: 0.4854 (OUTLIER) cc_final: 0.4630 (mp) REVERT: B 719 TRP cc_start: 0.6305 (t60) cc_final: 0.5831 (t60) REVERT: B 939 ASP cc_start: 0.6948 (m-30) cc_final: 0.6666 (m-30) REVERT: B 1187 LEU cc_start: 0.2395 (OUTLIER) cc_final: 0.1849 (pp) REVERT: B 1301 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.4878 (m-80) REVERT: B 1332 ASP cc_start: 0.0569 (OUTLIER) cc_final: 0.0366 (t70) REVERT: J 109 ASP cc_start: 0.5860 (OUTLIER) cc_final: 0.5301 (p0) REVERT: J 250 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.5841 (mtt180) outliers start: 181 outliers final: 105 residues processed: 403 average time/residue: 1.2311 time to fit residues: 592.3955 Evaluate side-chains 362 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 230 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 ASN 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 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 106 VAL 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 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 20 ARG Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 81 GLU 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 205 THR Chi-restraints excluded: chain G residue 218 THR 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 314 THR Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 196 LYS 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 662 LEU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE 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 860 MET 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 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1040 VAL 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 283 THR Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG 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 176 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 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 656 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 858 THR Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1332 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 250 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 0.0570 chunk 135 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 50.0000 chunk 266 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 GLN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN B 801 ASN ** B1234 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 28507 Z= 0.166 Angle : 0.573 11.365 38588 Z= 0.295 Chirality : 0.042 0.290 4263 Planarity : 0.004 0.076 5006 Dihedral : 6.926 89.225 3966 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 4.91 % Allowed : 31.32 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3487 helix: 0.96 (0.13), residues: 1753 sheet: 0.01 (0.26), residues: 374 loop : -1.57 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 261 HIS 0.007 0.001 HIS H 220 PHE 0.018 0.001 PHE A1017 TYR 0.023 0.001 TYR B 682 ARG 0.013 0.000 ARG I 168 *********************** REFINEMENT MACRO_CYCLE 8 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 387 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 247 time to evaluate : 2.955 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: F 47 MET cc_start: 0.7693 (mtp) cc_final: 0.7301 (mtp) REVERT: F 179 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6835 (mtm180) REVERT: F 356 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6974 (mtt-85) REVERT: G 95 GLU cc_start: 0.7570 (mp0) cc_final: 0.6967 (pm20) REVERT: G 240 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: G 375 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7139 (p0) REVERT: I 80 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8195 (mp) REVERT: I 138 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8237 (tm) REVERT: I 196 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8383 (pttt) REVERT: A 735 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7701 (p0) REVERT: A 801 ASN cc_start: 0.6911 (OUTLIER) cc_final: 0.6540 (m-40) REVERT: A 860 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6978 (mtm) REVERT: A 1062 GLU cc_start: 0.2017 (OUTLIER) cc_final: 0.1133 (tp30) REVERT: A 1289 GLN cc_start: 0.8953 (mt0) cc_final: 0.8461 (mt0) REVERT: H 215 CYS cc_start: 0.3820 (OUTLIER) cc_final: 0.2991 (p) REVERT: H 224 GLN cc_start: 0.7553 (mm-40) cc_final: 0.6924 (mm110) REVERT: H 259 THR cc_start: 0.8174 (t) cc_final: 0.7961 (m) REVERT: C 21 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7839 (t80) REVERT: C 55 LYS cc_start: 0.7363 (mmtt) cc_final: 0.7028 (mmmt) REVERT: C 76 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: E 32 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7041 (ttp-170) REVERT: E 56 GLU cc_start: 0.6757 (mp0) cc_final: 0.6325 (mt-10) REVERT: B 648 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7052 (t) REVERT: B 716 LEU cc_start: 0.4774 (OUTLIER) cc_final: 0.4569 (mp) REVERT: B 719 TRP cc_start: 0.6386 (t60) cc_final: 0.5939 (t60) REVERT: B 773 MET cc_start: 0.6063 (tpp) cc_final: 0.5719 (tpt) REVERT: B 939 ASP cc_start: 0.6977 (m-30) cc_final: 0.6692 (m-30) REVERT: B 1187 LEU cc_start: 0.2278 (OUTLIER) cc_final: 0.1735 (pp) REVERT: B 1226 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: B 1301 PHE cc_start: 0.5414 (OUTLIER) cc_final: 0.4829 (m-80) REVERT: B 1332 ASP cc_start: 0.0554 (OUTLIER) cc_final: 0.0352 (t70) REVERT: J 109 ASP cc_start: 0.5936 (OUTLIER) cc_final: 0.5390 (p0) outliers start: 140 outliers final: 86 residues processed: 368 average time/residue: 1.2560 time to fit residues: 549.0921 Evaluate side-chains 343 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 235 time to evaluate : 3.163 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 106 VAL 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 356 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 81 GLU 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 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 375 ASN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 196 LYS 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 687 LYS Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 801 ASN 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 860 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 GLU 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 215 CYS Chi-restraints excluded: chain H residue 299 VAL 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 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 73 GLU 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 160 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1226 GLU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1332 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 218 LEU 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 272 ILE Chi-restraints excluded: chain J residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 1.9990 chunk 325 optimal weight: 5.9990 chunk 296 optimal weight: 0.6980 chunk 316 optimal weight: 0.9980 chunk 324 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 299 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN J 79 HIS J 183 HIS ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 28507 Z= 0.189 Angle : 0.586 11.749 38588 Z= 0.301 Chirality : 0.042 0.231 4263 Planarity : 0.004 0.075 5006 Dihedral : 6.863 88.681 3963 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.90 % Rotamer: Outliers : 4.84 % Allowed : 31.25 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3487 helix: 0.98 (0.13), residues: 1753 sheet: 0.07 (0.26), residues: 374 loop : -1.54 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 261 HIS 0.007 0.001 HIS H 220 PHE 0.024 0.001 PHE A1305 TYR 0.022 0.001 TYR B 682 ARG 0.014 0.000 ARG I 168 *********************** REFINEMENT MACRO_CYCLE 9 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 377 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 239 time to evaluate : 3.249 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: F 47 MET cc_start: 0.7767 (mtp) cc_final: 0.7371 (mtp) REVERT: F 179 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6864 (mtm180) REVERT: G 95 GLU cc_start: 0.7525 (mp0) cc_final: 0.7221 (mp0) REVERT: G 240 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: G 375 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7177 (p0) REVERT: I 138 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8244 (tm) REVERT: I 196 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8413 (pttt) REVERT: A 735 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7709 (p0) REVERT: A 801 ASN cc_start: 0.7026 (OUTLIER) cc_final: 0.6634 (m-40) REVERT: A 860 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6987 (mtm) REVERT: A 1062 GLU cc_start: 0.1992 (OUTLIER) cc_final: 0.1078 (tp30) REVERT: H 224 GLN cc_start: 0.7576 (mm-40) cc_final: 0.6922 (mm110) REVERT: H 259 THR cc_start: 0.8163 (t) cc_final: 0.7908 (m) REVERT: C 21 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7843 (t80) REVERT: C 55 LYS cc_start: 0.7350 (mmtt) cc_final: 0.7010 (mmmt) REVERT: C 76 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: C 110 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7524 (t) REVERT: E 32 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7053 (ttp-170) REVERT: E 56 GLU cc_start: 0.6757 (mp0) cc_final: 0.6349 (mt-10) REVERT: B 648 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.7067 (t) REVERT: B 716 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.4577 (mp) REVERT: B 719 TRP cc_start: 0.6383 (t60) cc_final: 0.5941 (t60) REVERT: B 773 MET cc_start: 0.6046 (tpp) cc_final: 0.5683 (tpt) REVERT: B 939 ASP cc_start: 0.7077 (m-30) cc_final: 0.6791 (m-30) REVERT: B 1187 LEU cc_start: 0.2253 (OUTLIER) cc_final: 0.1734 (pp) REVERT: B 1301 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.4836 (m-80) REVERT: B 1332 ASP cc_start: 0.0815 (OUTLIER) cc_final: 0.0589 (t70) REVERT: J 109 ASP cc_start: 0.5943 (OUTLIER) cc_final: 0.5398 (p0) outliers start: 138 outliers final: 94 residues processed: 360 average time/residue: 1.2363 time to fit residues: 529.0390 Evaluate side-chains 347 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 234 time to evaluate : 3.482 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 106 VAL 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 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 81 GLU 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 180 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain G residue 360 MET 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 196 LYS 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 687 LYS Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 801 ASN 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 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 GLU 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 299 VAL 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 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 90 THR 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 176 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 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 656 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1301 PHE Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1332 ASP Chi-restraints excluded: chain B residue 1341 TYR Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 218 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 334 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 279 optimal weight: 0.0670 chunk 28 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 231 ASN G 72 GLN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 402 GLN ** B 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28507 Z= 0.325 Angle : 0.681 16.572 38588 Z= 0.349 Chirality : 0.046 0.337 4263 Planarity : 0.005 0.078 5006 Dihedral : 7.243 87.875 3962 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.85 % Favored : 94.01 % Rotamer: Outliers : 4.45 % Allowed : 31.95 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.15 % 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: -0.45 (0.14), residues: 3487 helix: 0.64 (0.12), residues: 1756 sheet: -0.00 (0.26), residues: 377 loop : -1.62 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 261 HIS 0.009 0.001 HIS H 220 PHE 0.026 0.002 PHE D 95 TYR 0.024 0.002 TYR B 682 ARG 0.013 0.001 ARG I 168 ********************** REFINEMENT MACRO_CYCLE 10 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 364 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 237 time to evaluate : 3.427 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: F 179 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6840 (mtm180) REVERT: G 95 GLU cc_start: 0.7561 (mp0) cc_final: 0.7233 (mp0) REVERT: G 240 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: G 375 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7338 (p0) REVERT: I 196 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8412 (pttt) REVERT: A 735 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7673 (p0) REVERT: A 801 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7052 (m-40) REVERT: A 860 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7052 (mtm) REVERT: A 1062 GLU cc_start: 0.2142 (OUTLIER) cc_final: 0.1057 (tp30) REVERT: A 1289 GLN cc_start: 0.8904 (mt0) cc_final: 0.8481 (mt0) REVERT: H 224 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7044 (mm110) REVERT: H 259 THR cc_start: 0.8163 (t) cc_final: 0.7878 (m) REVERT: C 21 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7968 (t80) REVERT: C 55 LYS cc_start: 0.7434 (mmtt) cc_final: 0.6962 (mmmt) REVERT: C 76 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 716 LEU cc_start: 0.4906 (OUTLIER) cc_final: 0.4671 (mp) REVERT: B 719 TRP cc_start: 0.6270 (t60) cc_final: 0.5810 (t60) REVERT: B 773 MET cc_start: 0.6296 (tpp) cc_final: 0.5924 (tpt) REVERT: B 939 ASP cc_start: 0.7084 (m-30) cc_final: 0.6781 (m-30) REVERT: B 942 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7446 (tt) REVERT: B 1301 PHE cc_start: 0.5566 (OUTLIER) cc_final: 0.4977 (m-80) REVERT: J 109 ASP cc_start: 0.5935 (OUTLIER) cc_final: 0.5411 (p0) outliers start: 127 outliers final: 96 residues processed: 349 average time/residue: 1.2434 time to fit residues: 515.4921 Evaluate side-chains 348 residues out of total 3229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 238 time to evaluate : 3.426 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 106 VAL 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 G residue 2 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 81 GLU 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 205 THR Chi-restraints excluded: chain G residue 218 THR 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 314 THR Chi-restraints excluded: chain G residue 360 MET 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 171 ASP Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 196 LYS 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 687 LYS Chi-restraints excluded: chain A residue 701 ASP Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 801 ASN 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 889 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 GLU 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 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 54 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 90 THR 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 176 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 231 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 656 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1134 SER 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 63 ASP Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 218 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 297 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 235 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 402 GLN E 192 ASN ** B 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS ** J 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.185937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.133863 restraints weight = 40061.448| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.54 r_work: 0.3786 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 28507 Z= 0.191 Angle : 0.614 15.518 38588 Z= 0.314 Chirality : 0.043 0.307 4263 Planarity : 0.004 0.077 5006 Dihedral : 7.031 87.291 3962 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 4.17 % Allowed : 32.27 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.15 % 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: -0.24 (0.14), residues: 3487 helix: 0.85 (0.13), residues: 1753 sheet: 0.00 (0.26), residues: 373 loop : -1.54 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 261 HIS 0.007 0.001 HIS I 173 PHE 0.024 0.001 PHE A1305 TYR 0.022 0.001 TYR B 682 ARG 0.014 0.000 ARG I 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12763.89 seconds wall clock time: 226 minutes 9.94 seconds (13569.94 seconds total)