Starting phenix.real_space_refine on Fri Aug 9 22:10:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9f_37367/08_2024/8w9f_37367_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9f_37367/08_2024/8w9f_37367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9f_37367/08_2024/8w9f_37367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9f_37367/08_2024/8w9f_37367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9f_37367/08_2024/8w9f_37367_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9f_37367/08_2024/8w9f_37367_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 292 5.49 5 S 104 5.16 5 C 16800 2.51 5 N 4889 2.21 5 O 5776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 698": "OD1" <-> "OD2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 818": "OD1" <-> "OD2" Residue "A TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 958": "OD1" <-> "OD2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 981": "OD1" <-> "OD2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1006": "OD1" <-> "OD2" Residue "A ASP 1012": "OD1" <-> "OD2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A TYR 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1067": "OD1" <-> "OD2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1160": "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 ASP 1197": "OD1" <-> "OD2" Residue "A PHE 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1259": "OD1" <-> "OD2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1331": "OE1" <-> "OE2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A TYR 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E ASP 300": "OD1" <-> "OD2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 359": "OE1" <-> "OE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 496": "NH1" <-> "NH2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 550": "OD1" <-> "OD2" Residue "E PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 571": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 258": "OE1" <-> "OE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 374": "OD1" <-> "OD2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 544": "OE1" <-> "OE2" Residue "F ASP 550": "OD1" <-> "OD2" Residue "F PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 553": "OD1" <-> "OD2" Residue "F TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 575": "OD1" <-> "OD2" Residue "a TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "a ASP 106": "OD1" <-> "OD2" Residue "a ARG 134": "NH1" <-> "NH2" Residue "b ASP 24": "OD1" <-> "OD2" Residue "b GLU 52": "OE1" <-> "OE2" Residue "b GLU 63": "OE1" <-> "OE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 74": "OE1" <-> "OE2" Residue "b TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c ASP 90": "OD1" <-> "OD2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 68": "OD1" <-> "OD2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 50": "OE1" <-> "OE2" Residue "e TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 59": "OE1" <-> "OE2" Residue "e PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 105": "OE1" <-> "OE2" Residue "e ASP 106": "OD1" <-> "OD2" Residue "f TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g GLU 64": "OE1" <-> "OE2" Residue "g GLU 91": "OE1" <-> "OE2" Residue "h TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 51": "OD1" <-> "OD2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27868 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5066 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2884 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "D" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1282 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "c" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "f" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "g" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "i" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "j" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "G" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 570 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 2 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5538 SG CYS E 263 92.341 97.136 91.981 1.00 63.46 S ATOM 5555 SG CYS E 266 89.928 95.114 93.570 1.00 53.02 S ATOM 5708 SG CYS E 286 93.231 93.681 92.999 1.00 38.07 S ATOM 5619 SG CYS E 275 100.350 102.730 82.033 1.00 87.52 S ATOM 5640 SG CYS E 278 96.846 101.994 81.535 1.00 89.24 S ATOM 5843 SG CYS E 303 98.070 98.765 80.999 1.00 84.64 S ATOM 5866 SG CYS E 306 98.964 101.341 78.710 1.00 85.05 S ATOM 6956 SG CYS E 440 60.182 85.037 111.606 1.00 27.99 S ATOM 6982 SG CYS E 443 58.098 82.201 111.670 1.00 23.37 S ATOM 7170 SG CYS E 466 59.127 83.512 115.391 1.00 25.28 S ATOM 6795 SG CYS E 420 53.575 85.172 126.282 1.00 30.63 S ATOM 7051 SG CYS E 451 57.050 84.408 125.918 1.00 26.14 S ATOM 14065 SG CYS F 263 43.423 37.948 66.888 1.00 95.21 S ATOM 14082 SG CYS F 266 44.744 34.700 67.224 1.00 88.26 S ATOM 14235 SG CYS F 286 42.230 36.473 69.982 1.00 90.91 S ATOM 14146 SG CYS F 275 40.471 50.443 63.991 1.00 96.38 S ATOM 14167 SG CYS F 278 43.804 49.392 64.497 1.00 89.68 S ATOM 14370 SG CYS F 303 43.056 49.359 68.089 1.00 96.28 S ATOM 14393 SG CYS F 306 42.764 52.457 65.952 1.00 88.14 S Time building chain proxies: 14.32, per 1000 atoms: 0.51 Number of scatterers: 27868 At special positions: 0 Unit cell: (144.571, 183.703, 168.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 104 16.00 P 292 15.00 O 5776 8.00 N 4889 7.00 C 16800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.72 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 466 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 286 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 266 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 263 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 306 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 303 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 278 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 275 " Number of angles added : 18 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 22 sheets defined 60.5% alpha, 4.7% beta 145 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 9.55 Creating SS restraints... Processing helix chain 'A' and resid 663 through 677 removed outlier: 3.543A pdb=" N THR A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.535A pdb=" N TYR A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.748A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.506A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 840 removed outlier: 3.767A pdb=" N ILE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 removed outlier: 3.578A pdb=" N ASN A 848 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 886 through 925 Proline residue: A 892 - end of helix removed outlier: 4.978A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.501A pdb=" N LEU A 933 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 3.899A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 3.859A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1025 through 1039 Processing helix chain 'A' and resid 1064 through 1070 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.626A pdb=" N ASN A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1141 through 1173 removed outlier: 5.041A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 3.833A pdb=" N LEU A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1217 removed outlier: 3.753A pdb=" N GLN A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1232 Processing helix chain 'A' and resid 1237 through 1240 Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.768A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 removed outlier: 3.509A pdb=" N ALA A1275 " --> pdb=" O LYS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.593A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1343 removed outlier: 3.992A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 315 through 330 Processing helix chain 'E' and resid 331 through 334 Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.547A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.731A pdb=" N ASN E 433 " --> pdb=" O HIS E 430 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER E 434 " --> pdb=" O PRO E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 430 through 434' Processing helix chain 'E' and resid 543 through 580 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.148A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.703A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.622A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 61 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.849A pdb=" N LYS B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.580A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 301 removed outlier: 4.425A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 271 through 297 removed outlier: 5.390A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.923A pdb=" N LEU C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Proline residue: C 339 - end of helix Processing helix chain 'C' and resid 348 through 369 Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 271 through 294 removed outlier: 3.536A pdb=" N GLN D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 316 removed outlier: 4.171A pdb=" N GLN D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.764A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 375 removed outlier: 3.716A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 removed outlier: 3.565A pdb=" N ASP D 384 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.576A pdb=" N GLU D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 344 removed outlier: 4.647A pdb=" N LYS F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 544 through 577 removed outlier: 3.606A pdb=" N LEU F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.898A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.585A pdb=" N ALA a 114 " --> pdb=" O CYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.539A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.839A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.670A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.554A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN c 73 " --> pdb=" O ALA c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.645A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 removed outlier: 3.569A pdb=" N LEU c 115 " --> pdb=" O GLN c 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 removed outlier: 3.719A pdb=" N ASN d 84 " --> pdb=" O LEU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 124 removed outlier: 4.104A pdb=" N ALA d 124 " --> pdb=" O LYS d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 removed outlier: 3.897A pdb=" N LEU e 48 " --> pdb=" O GLY e 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER e 57 " --> pdb=" O ARG e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.688A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.583A pdb=" N ALA e 114 " --> pdb=" O CYS e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 131 removed outlier: 3.540A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.505A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.806A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG f 67 " --> pdb=" O GLU f 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.531A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.694A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 removed outlier: 3.595A pdb=" N ILE h 94 " --> pdb=" O THR h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 124 removed outlier: 3.752A pdb=" N SER h 123 " --> pdb=" O THR h 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.610A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 178 through 179 removed outlier: 3.808A pdb=" N GLU B 62 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA7, first strand: chain 'E' and resid 521 through 522 removed outlier: 6.181A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'F' and resid 272 through 274 Processing sheet with id=AB2, first strand: chain 'F' and resid 364 through 366 Processing sheet with id=AB3, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.140A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'c' and resid 77 through 78 removed outlier: 3.719A pdb=" N ILE c 78 " --> pdb=" O GLY d 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.680A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.832A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.373A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'g' and resid 77 through 78 removed outlier: 3.608A pdb=" N ILE g 78 " --> pdb=" O GLY h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.853A pdb=" N CYS G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE G 78 " --> pdb=" O LEU G 28 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 698 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 16.99 Time building geometry restraints manager: 14.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.45: 13581 1.45 - 1.77: 15291 1.77 - 2.08: 159 2.08 - 2.40: 1 2.40 - 2.72: 1 Bond restraints: 29033 Sorted by residual: bond pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 1.512 2.718 -1.206 2.20e-02 2.07e+03 3.00e+03 bond pdb=" CE3 TRP D 236 " pdb=" CZ3 TRP D 236 " ideal model delta sigma weight residual 1.382 2.269 -0.887 3.00e-02 1.11e+03 8.74e+02 bond pdb=" CE2 TRP D 236 " pdb=" CZ2 TRP D 236 " ideal model delta sigma weight residual 1.394 1.823 -0.429 2.10e-02 2.27e+03 4.18e+02 bond pdb=" CZ3 TRP D 236 " pdb=" CH2 TRP D 236 " ideal model delta sigma weight residual 1.400 1.853 -0.453 2.50e-02 1.60e+03 3.28e+02 bond pdb=" N PRO c 117 " pdb=" CA PRO c 117 " ideal model delta sigma weight residual 1.466 1.690 -0.224 1.24e-02 6.50e+03 3.26e+02 ... (remaining 29028 not shown) Histogram of bond angle deviations from ideal: 92.35 - 102.29: 448 102.29 - 112.23: 16137 112.23 - 122.17: 18974 122.17 - 132.11: 4771 132.11 - 142.05: 117 Bond angle restraints: 40447 Sorted by residual: angle pdb=" C ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta sigma weight residual 109.65 142.05 -32.40 1.74e+00 3.30e-01 3.47e+02 angle pdb=" C LEU c 116 " pdb=" N PRO c 117 " pdb=" CA PRO c 117 " ideal model delta sigma weight residual 119.78 138.57 -18.79 1.03e+00 9.43e-01 3.33e+02 angle pdb=" C LYS B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.89 134.57 -14.68 1.02e+00 9.61e-01 2.07e+02 angle pdb=" C LYS B 41 " pdb=" N PRO B 42 " pdb=" CA PRO B 42 " ideal model delta sigma weight residual 119.87 133.85 -13.98 1.04e+00 9.25e-01 1.81e+02 angle pdb=" CA TYR F 372 " pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 113.90 136.95 -23.05 1.80e+00 3.09e-01 1.64e+02 ... (remaining 40442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12580 17.88 - 35.77: 2320 35.77 - 53.65: 1420 53.65 - 71.53: 475 71.53 - 89.42: 43 Dihedral angle restraints: 16838 sinusoidal: 8930 harmonic: 7908 Sorted by residual: dihedral pdb=" C ARG E 384 " pdb=" N ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta harmonic sigma weight residual -122.60 -155.40 32.80 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" C THR E 169 " pdb=" N THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual -122.00 -152.32 30.32 0 2.50e+00 1.60e-01 1.47e+02 dihedral pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual 123.40 151.08 -27.68 0 2.50e+00 1.60e-01 1.23e+02 ... (remaining 16835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 4425 0.239 - 0.479: 32 0.479 - 0.718: 5 0.718 - 0.957: 2 0.957 - 1.197: 2 Chirality restraints: 4466 Sorted by residual: chirality pdb=" CA THR E 169 " pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CB THR E 169 " both_signs ideal model delta sigma weight residual False 2.53 1.33 1.20 2.00e-01 2.50e+01 3.58e+01 chirality pdb=" CA ARG E 384 " pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CB ARG E 384 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA ASP E 383 " pdb=" N ASP E 383 " pdb=" C ASP E 383 " pdb=" CB ASP E 383 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 4463 not shown) Planarity restraints: 4129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 157 " 0.029 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C ALA B 157 " -0.101 2.00e-02 2.50e+03 pdb=" O ALA B 157 " 0.039 2.00e-02 2.50e+03 pdb=" N SER B 158 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 66 " 0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C ALA B 66 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA B 66 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS B 67 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 470 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E 471 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO E 471 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 471 " 0.061 5.00e-02 4.00e+02 ... (remaining 4126 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 10 1.91 - 2.65: 757 2.65 - 3.40: 37779 3.40 - 4.15: 71081 4.15 - 4.90: 119842 Nonbonded interactions: 229469 Sorted by model distance: nonbonded pdb=" CB SER E 179 " pdb=" OE2 GLU B 129 " model vdw 1.158 3.440 nonbonded pdb=" OE2 GLU A 904 " pdb=" ND2 ASN E 116 " model vdw 1.174 3.120 nonbonded pdb=" NZ LYS B 41 " pdb=" SD MET B 315 " model vdw 1.548 3.480 nonbonded pdb=" CG2 THR E 169 " pdb=" CB MET B 53 " model vdw 1.581 3.860 nonbonded pdb=" O SER E 179 " pdb=" OE1 GLU B 129 " model vdw 1.728 3.040 ... (remaining 229464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 219 through 401) } ncs_group { reference = chain 'a' selection = (chain 'e' and resid 38 through 134) } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 24 through 102) } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } ncs_group { reference = (chain 'i' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'j' and (resid -73 through -1 or resid 1 through 73)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 90.550 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4241 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 : 0.012 1.206 29033 Z= 0.619 Angle : 0.983 32.398 40447 Z= 0.622 Chirality : 0.064 1.197 4466 Planarity : 0.006 0.114 4129 Dihedral : 24.101 89.417 11728 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.57 % Favored : 94.90 % Rotamer: Outliers : 7.51 % Allowed : 16.82 % Favored : 75.67 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 2646 helix: -0.63 (0.12), residues: 1500 sheet: -1.14 (0.45), residues: 125 loop : -2.46 (0.16), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP G 31 HIS 0.009 0.001 HIS G 18 PHE 0.048 0.002 PHE E 387 TYR 0.053 0.002 TYR G 100 ARG 0.010 0.001 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 457 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 778 LEU cc_start: 0.6060 (mm) cc_final: 0.5125 (mm) REVERT: A 903 GLU cc_start: 0.1730 (OUTLIER) cc_final: 0.0956 (mt-10) REVERT: A 1065 LEU cc_start: -0.4742 (OUTLIER) cc_final: -0.5544 (mp) REVERT: A 1332 ASP cc_start: 0.0726 (t0) cc_final: 0.0447 (m-30) REVERT: A 1345 HIS cc_start: -0.1069 (t-90) cc_final: -0.1315 (m170) REVERT: E 108 VAL cc_start: 0.2626 (OUTLIER) cc_final: 0.2259 (m) REVERT: E 123 ILE cc_start: -0.1158 (OUTLIER) cc_final: -0.1539 (mm) REVERT: E 272 PHE cc_start: 0.2359 (OUTLIER) cc_final: 0.2004 (p90) REVERT: E 387 PHE cc_start: 0.1003 (OUTLIER) cc_final: 0.0561 (p90) REVERT: E 388 ASN cc_start: 0.2422 (OUTLIER) cc_final: 0.1934 (t0) REVERT: B 2 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.3208 (t) REVERT: B 14 LYS cc_start: -0.0227 (OUTLIER) cc_final: -0.1076 (mtpt) REVERT: B 32 TYR cc_start: 0.2204 (OUTLIER) cc_final: 0.0780 (m-80) REVERT: B 38 HIS cc_start: 0.3201 (OUTLIER) cc_final: 0.2201 (m170) REVERT: B 93 ASN cc_start: 0.3600 (p0) cc_final: 0.3360 (p0) REVERT: B 111 PRO cc_start: -0.0664 (OUTLIER) cc_final: -0.0932 (Cg_exo) REVERT: B 112 VAL cc_start: 0.1354 (OUTLIER) cc_final: 0.0976 (m) REVERT: B 187 VAL cc_start: 0.5049 (p) cc_final: 0.4322 (p) REVERT: B 204 MET cc_start: 0.3062 (ttt) cc_final: 0.2684 (ttm) REVERT: C 222 LEU cc_start: 0.0502 (OUTLIER) cc_final: 0.0263 (tp) REVERT: C 235 ASP cc_start: -0.1351 (OUTLIER) cc_final: -0.2202 (t0) REVERT: C 241 LYS cc_start: -0.0648 (OUTLIER) cc_final: -0.1225 (mttt) REVERT: C 376 ASP cc_start: -0.1500 (OUTLIER) cc_final: -0.2485 (p0) REVERT: D 332 LEU cc_start: 0.2591 (OUTLIER) cc_final: 0.1974 (mp) REVERT: F 343 ILE cc_start: 0.0584 (mt) cc_final: -0.0309 (mp) REVERT: a 86 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.7964 (t) REVERT: a 89 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8601 (m) REVERT: b 58 LEU cc_start: 0.8296 (tp) cc_final: 0.8089 (tt) REVERT: b 88 TYR cc_start: 0.6500 (m-10) cc_final: 0.6238 (m-10) REVERT: c 30 VAL cc_start: 0.8496 (t) cc_final: 0.8226 (p) REVERT: c 62 ILE cc_start: 0.8790 (tt) cc_final: 0.8212 (mt) REVERT: c 90 ASP cc_start: 0.7134 (t0) cc_final: 0.6906 (t0) REVERT: c 107 VAL cc_start: 0.8332 (m) cc_final: 0.8051 (t) REVERT: d 79 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7802 (mmm160) REVERT: e 60 LEU cc_start: 0.8374 (mt) cc_final: 0.8163 (mm) REVERT: e 87 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8395 (t) REVERT: f 84 MET cc_start: 0.7618 (mmm) cc_final: 0.6637 (tpp) REVERT: h 83 TYR cc_start: 0.7780 (m-10) cc_final: 0.7358 (m-10) REVERT: h 101 LEU cc_start: 0.8847 (mt) cc_final: 0.8409 (tp) outliers start: 180 outliers final: 25 residues processed: 607 average time/residue: 0.4372 time to fit residues: 400.3120 Evaluate side-chains 230 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 184 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 226 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS A 884 HIS A 965 HIS A1004 ASN A1137 ASN A1163 GLN A1315 GLN E 304 ASN E 314 ASN E 346 HIS E 350 GLN E 352 GLN E 376 ASN E 459 ASN E 541 GLN E 580 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 380 ASN C 389 ASN C 393 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 380 ASN D 393 GLN F 346 HIS F 355 ASN ** a 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 HIS d 95 GLN e 125 GLN f 25 ASN ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4595 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.206 29033 Z= 0.522 Angle : 0.784 23.233 40447 Z= 0.435 Chirality : 0.044 0.205 4466 Planarity : 0.006 0.089 4129 Dihedral : 26.631 88.547 6239 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.91 % Favored : 94.86 % Rotamer: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 2646 helix: 0.45 (0.12), residues: 1551 sheet: -0.64 (0.45), residues: 121 loop : -2.09 (0.17), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 916 HIS 0.011 0.002 HIS B 150 PHE 0.027 0.003 PHE A 819 TYR 0.029 0.002 TYR g 50 ARG 0.007 0.001 ARG e 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1332 ASP cc_start: 0.0738 (t0) cc_final: 0.0379 (m-30) REVERT: E 459 ASN cc_start: 0.4434 (t0) cc_final: 0.4128 (m110) REVERT: E 517 ASN cc_start: -0.1331 (OUTLIER) cc_final: -0.1603 (t0) REVERT: B 45 ILE cc_start: 0.6147 (mt) cc_final: 0.5908 (tt) REVERT: B 93 ASN cc_start: 0.3494 (p0) cc_final: 0.2973 (p0) REVERT: C 401 MET cc_start: 0.1600 (tpt) cc_final: 0.1251 (tpp) REVERT: F 328 LYS cc_start: 0.5729 (tptm) cc_final: 0.3950 (pttt) REVERT: F 365 LYS cc_start: 0.1551 (ptpt) cc_final: 0.1106 (ttpp) REVERT: c 38 ASN cc_start: 0.8314 (m110) cc_final: 0.8038 (m-40) REVERT: d 116 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7827 (tttp) REVERT: e 60 LEU cc_start: 0.7963 (mt) cc_final: 0.7295 (pp) REVERT: f 84 MET cc_start: 0.7451 (mmm) cc_final: 0.7249 (tpp) REVERT: h 62 MET cc_start: 0.8407 (mmm) cc_final: 0.8134 (mmm) REVERT: h 101 LEU cc_start: 0.8745 (mt) cc_final: 0.8396 (tp) outliers start: 5 outliers final: 1 residues processed: 228 average time/residue: 0.4327 time to fit residues: 157.0455 Evaluate side-chains 142 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 284 optimal weight: 30.0000 chunk 234 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 ASN A1137 ASN A1216 ASN E 174 ASN ** E 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 HIS a 113 HIS ** c 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4777 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.204 29033 Z= 0.544 Angle : 0.793 23.752 40447 Z= 0.441 Chirality : 0.044 0.249 4466 Planarity : 0.006 0.082 4129 Dihedral : 27.110 89.892 6239 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 0.13 % Allowed : 4.47 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.66 (0.15), residues: 2646 helix: 0.51 (0.13), residues: 1542 sheet: -0.64 (0.44), residues: 119 loop : -1.93 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 236 HIS 0.011 0.002 HIS E 448 PHE 0.036 0.003 PHE B 284 TYR 0.034 0.003 TYR B 346 ARG 0.019 0.001 ARG E 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ILE cc_start: 0.6419 (mt) cc_final: 0.6182 (tt) REVERT: B 93 ASN cc_start: 0.3668 (p0) cc_final: 0.3338 (p0) REVERT: B 288 MET cc_start: 0.2792 (ttm) cc_final: 0.2542 (ttp) REVERT: B 305 MET cc_start: 0.6680 (tpt) cc_final: 0.6280 (tpp) REVERT: F 365 LYS cc_start: 0.1834 (ptmt) cc_final: 0.1106 (ttpp) REVERT: b 85 ASP cc_start: 0.8442 (m-30) cc_final: 0.8216 (p0) REVERT: b 88 TYR cc_start: 0.6737 (m-10) cc_final: 0.5938 (m-10) REVERT: c 38 ASN cc_start: 0.8076 (m110) cc_final: 0.7479 (m-40) REVERT: c 62 ILE cc_start: 0.8903 (mm) cc_final: 0.8693 (tt) REVERT: e 60 LEU cc_start: 0.7815 (mt) cc_final: 0.7084 (pp) REVERT: e 105 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7327 (tm-30) REVERT: h 101 LEU cc_start: 0.8689 (mt) cc_final: 0.8424 (tp) REVERT: G 107 MET cc_start: 0.6163 (ttm) cc_final: 0.5772 (ttp) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.3939 time to fit residues: 120.9211 Evaluate side-chains 142 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 HIS ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN E 302 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS a 125 GLN c 38 ASN f 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4732 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29033 Z= 0.484 Angle : 0.664 23.587 40447 Z= 0.376 Chirality : 0.040 0.239 4466 Planarity : 0.005 0.066 4129 Dihedral : 26.796 89.629 6239 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.12 (0.16), residues: 2646 helix: 0.96 (0.13), residues: 1524 sheet: -0.43 (0.46), residues: 117 loop : -1.67 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 236 HIS 0.014 0.001 HIS E 448 PHE 0.032 0.002 PHE E 567 TYR 0.026 0.002 TYR F 372 ARG 0.008 0.001 ARG A1009 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 2.894 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: A 1071 ARG cc_start: 0.2694 (mpp-170) cc_final: 0.1226 (tpt170) REVERT: E 387 PHE cc_start: 0.1016 (OUTLIER) cc_final: 0.0531 (m-10) REVERT: E 404 ASP cc_start: 0.4258 (p0) cc_final: 0.3999 (p0) REVERT: B 45 ILE cc_start: 0.6261 (mt) cc_final: 0.6022 (tt) REVERT: B 93 ASN cc_start: 0.3187 (p0) cc_final: 0.2886 (p0) REVERT: C 311 LYS cc_start: 0.0269 (mttt) cc_final: -0.0623 (tptm) REVERT: F 365 LYS cc_start: 0.1738 (ptmt) cc_final: 0.1125 (ttpp) REVERT: F 560 MET cc_start: 0.2347 (tpt) cc_final: 0.1043 (ttp) REVERT: b 58 LEU cc_start: 0.8879 (tp) cc_final: 0.8580 (tp) REVERT: c 92 GLU cc_start: 0.6196 (pt0) cc_final: 0.5367 (pt0) REVERT: d 62 MET cc_start: 0.8565 (mmm) cc_final: 0.8200 (mmm) REVERT: e 60 LEU cc_start: 0.7764 (mt) cc_final: 0.7157 (pp) REVERT: f 84 MET cc_start: 0.7207 (tpp) cc_final: 0.6995 (tpp) REVERT: g 56 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8262 (mm-30) REVERT: h 101 LEU cc_start: 0.8646 (mt) cc_final: 0.8367 (tp) REVERT: G 109 LYS cc_start: 0.5780 (ptpp) cc_final: 0.5543 (tppt) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.4002 time to fit residues: 117.7836 Evaluate side-chains 142 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 0.9990 chunk 158 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 193 optimal weight: 0.3980 chunk 0 optimal weight: 40.0000 chunk 142 optimal weight: 0.2980 chunk 250 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN E 302 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS F 346 HIS a 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4644 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.204 29033 Z= 0.461 Angle : 0.603 23.475 40447 Z= 0.346 Chirality : 0.038 0.185 4466 Planarity : 0.004 0.053 4129 Dihedral : 26.372 88.759 6239 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.34 (0.16), residues: 2646 helix: 1.33 (0.13), residues: 1548 sheet: -0.25 (0.46), residues: 117 loop : -1.54 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 236 HIS 0.006 0.001 HIS E 448 PHE 0.037 0.001 PHE E 567 TYR 0.023 0.001 TYR F 372 ARG 0.006 0.000 ARG F 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1071 ARG cc_start: 0.2486 (mpp-170) cc_final: 0.1082 (tpt170) REVERT: E 387 PHE cc_start: 0.1041 (p90) cc_final: 0.0724 (m-10) REVERT: E 564 ARG cc_start: 0.3854 (mtp85) cc_final: 0.3483 (mpt180) REVERT: B 45 ILE cc_start: 0.6807 (mt) cc_final: 0.6373 (tt) REVERT: F 328 LYS cc_start: 0.6116 (tptm) cc_final: 0.4210 (pttt) REVERT: F 365 LYS cc_start: 0.1704 (ptmt) cc_final: 0.1085 (ttpp) REVERT: b 58 LEU cc_start: 0.8845 (tp) cc_final: 0.8525 (tp) REVERT: c 90 ASP cc_start: 0.7501 (t0) cc_final: 0.6566 (t0) REVERT: e 60 LEU cc_start: 0.7664 (mt) cc_final: 0.7135 (pp) REVERT: g 56 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8203 (mm-30) REVERT: h 59 MET cc_start: 0.6716 (tpp) cc_final: 0.6437 (tpp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3998 time to fit residues: 125.7586 Evaluate side-chains 148 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN a 125 GLN f 93 GLN h 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4759 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.205 29033 Z= 0.489 Angle : 0.654 23.602 40447 Z= 0.372 Chirality : 0.039 0.173 4466 Planarity : 0.005 0.060 4129 Dihedral : 26.612 89.964 6239 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2646 helix: 1.22 (0.13), residues: 1527 sheet: -0.39 (0.47), residues: 117 loop : -1.52 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 236 HIS 0.009 0.001 HIS E 448 PHE 0.024 0.002 PHE E 567 TYR 0.027 0.002 TYR F 372 ARG 0.010 0.001 ARG E 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.4579 (mtt) cc_final: 0.4132 (mtm) REVERT: E 387 PHE cc_start: 0.0464 (p90) cc_final: 0.0105 (t80) REVERT: E 438 MET cc_start: 0.1633 (mtm) cc_final: 0.1381 (mtm) REVERT: E 564 ARG cc_start: 0.4055 (mtp85) cc_final: 0.3351 (mpt180) REVERT: B 45 ILE cc_start: 0.6747 (mt) cc_final: 0.6380 (tt) REVERT: B 259 MET cc_start: 0.0337 (ppp) cc_final: 0.0042 (ppp) REVERT: C 356 ILE cc_start: 0.4502 (mm) cc_final: 0.4232 (mm) REVERT: F 365 LYS cc_start: 0.1820 (ptmt) cc_final: 0.1151 (ttpp) REVERT: a 52 ARG cc_start: 0.7423 (mmt90) cc_final: 0.6681 (mtp85) REVERT: b 58 LEU cc_start: 0.8967 (tp) cc_final: 0.8572 (tp) REVERT: b 88 TYR cc_start: 0.6813 (m-10) cc_final: 0.6059 (m-10) REVERT: e 60 LEU cc_start: 0.7389 (mt) cc_final: 0.6843 (pp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3732 time to fit residues: 106.0973 Evaluate side-chains 138 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 278 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 128 optimal weight: 0.0980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS E 444 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN B 189 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN d 82 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4670 moved from start: 0.7986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.204 29033 Z= 0.462 Angle : 0.599 23.536 40447 Z= 0.343 Chirality : 0.037 0.154 4466 Planarity : 0.004 0.055 4129 Dihedral : 26.215 87.847 6239 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2646 helix: 1.49 (0.13), residues: 1533 sheet: -0.41 (0.46), residues: 122 loop : -1.42 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 236 HIS 0.007 0.001 HIS E 448 PHE 0.022 0.001 PHE E 567 TYR 0.024 0.001 TYR F 372 ARG 0.009 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1071 ARG cc_start: 0.2486 (mpp-170) cc_final: 0.0958 (tpt170) REVERT: A 1164 MET cc_start: 0.4719 (mtt) cc_final: 0.4281 (mtm) REVERT: E 258 GLU cc_start: 0.2073 (tp30) cc_final: 0.0410 (mp0) REVERT: E 387 PHE cc_start: -0.0138 (p90) cc_final: -0.0456 (t80) REVERT: E 564 ARG cc_start: 0.4126 (mtp85) cc_final: 0.3654 (mpt180) REVERT: B 45 ILE cc_start: 0.6837 (mt) cc_final: 0.6410 (tt) REVERT: B 259 MET cc_start: 0.0329 (ppp) cc_final: 0.0077 (ppp) REVERT: F 365 LYS cc_start: 0.1678 (ptmt) cc_final: 0.1009 (ttpp) REVERT: a 52 ARG cc_start: 0.7481 (mmt90) cc_final: 0.6799 (mtp85) REVERT: b 88 TYR cc_start: 0.6478 (m-10) cc_final: 0.5966 (m-10) REVERT: c 90 ASP cc_start: 0.6838 (t0) cc_final: 0.6206 (t0) REVERT: c 92 GLU cc_start: 0.6523 (pm20) cc_final: 0.6047 (pm20) REVERT: c 93 LEU cc_start: 0.8390 (mm) cc_final: 0.8130 (mm) REVERT: e 60 LEU cc_start: 0.7319 (mt) cc_final: 0.6796 (pp) REVERT: e 105 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7533 (tm-30) REVERT: g 56 GLU cc_start: 0.9050 (mp0) cc_final: 0.8645 (mp0) REVERT: g 91 GLU cc_start: 0.8669 (pm20) cc_final: 0.7997 (mp0) REVERT: G 107 MET cc_start: 0.6439 (ttm) cc_final: 0.6135 (ttp) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.3835 time to fit residues: 117.9065 Evaluate side-chains 145 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS E 444 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN B 38 HIS ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN c 31 HIS c 38 ASN d 82 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4833 moved from start: 0.8728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.206 29033 Z= 0.508 Angle : 0.709 24.267 40447 Z= 0.399 Chirality : 0.042 0.187 4466 Planarity : 0.005 0.067 4129 Dihedral : 26.841 89.345 6239 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 0.08 % Allowed : 1.04 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2646 helix: 0.98 (0.13), residues: 1507 sheet: -0.67 (0.51), residues: 101 loop : -1.51 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 236 HIS 0.011 0.002 HIS E 448 PHE 0.017 0.002 PHE E 567 TYR 0.029 0.002 TYR F 372 ARG 0.007 0.001 ARG E 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.2039 (ptp) cc_final: 0.1537 (ptp) REVERT: A 1164 MET cc_start: 0.4698 (mtt) cc_final: 0.4368 (mtm) REVERT: A 1257 MET cc_start: 0.2590 (mtp) cc_final: 0.2324 (mtp) REVERT: E 258 GLU cc_start: 0.2226 (tp30) cc_final: 0.0422 (mp0) REVERT: E 387 PHE cc_start: 0.0494 (p90) cc_final: 0.0279 (m-80) REVERT: E 564 ARG cc_start: 0.4759 (mtp85) cc_final: 0.3961 (mpt180) REVERT: B 38 HIS cc_start: 0.3791 (OUTLIER) cc_final: 0.3363 (m90) REVERT: B 45 ILE cc_start: 0.6816 (mt) cc_final: 0.6404 (tt) REVERT: B 259 MET cc_start: 0.0451 (ppp) cc_final: -0.0055 (ppp) REVERT: C 311 LYS cc_start: -0.0018 (mttt) cc_final: -0.0897 (tptm) REVERT: C 356 ILE cc_start: 0.4133 (mm) cc_final: 0.3879 (mm) REVERT: F 256 ASP cc_start: 0.1424 (t0) cc_final: 0.1189 (p0) REVERT: F 365 LYS cc_start: 0.2174 (ptmt) cc_final: 0.1502 (ttpp) REVERT: F 576 LYS cc_start: 0.1470 (mmmt) cc_final: 0.0014 (mttt) REVERT: a 52 ARG cc_start: 0.7380 (mmt90) cc_final: 0.6671 (mtp85) REVERT: c 92 GLU cc_start: 0.6430 (pm20) cc_final: 0.5888 (pm20) REVERT: e 60 LEU cc_start: 0.7481 (mt) cc_final: 0.6864 (pp) REVERT: g 91 GLU cc_start: 0.8591 (pm20) cc_final: 0.8027 (mp0) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.3734 time to fit residues: 107.6148 Evaluate side-chains 144 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 0.0170 chunk 266 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 113 optimal weight: 30.0000 chunk 203 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 234 optimal weight: 0.3980 chunk 245 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS E 444 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN B 38 HIS ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 350 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 ASN F 346 HIS a 108 ASN c 38 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4689 moved from start: 0.8680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.204 29033 Z= 0.460 Angle : 0.605 23.975 40447 Z= 0.346 Chirality : 0.038 0.171 4466 Planarity : 0.004 0.058 4129 Dihedral : 26.234 87.590 6239 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2646 helix: 1.47 (0.13), residues: 1539 sheet: -0.78 (0.46), residues: 118 loop : -1.40 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 236 HIS 0.007 0.001 HIS C 369 PHE 0.023 0.001 PHE e 104 TYR 0.023 0.001 TYR F 372 ARG 0.005 0.000 ARG e 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.1789 (ptp) cc_final: 0.1351 (ptp) REVERT: A 1071 ARG cc_start: 0.2373 (mpp-170) cc_final: 0.0769 (tpt170) REVERT: A 1164 MET cc_start: 0.4740 (mtt) cc_final: 0.4354 (mtm) REVERT: E 258 GLU cc_start: 0.2032 (tp30) cc_final: 0.0510 (mp0) REVERT: E 564 ARG cc_start: 0.4526 (mtp85) cc_final: 0.3878 (mpt180) REVERT: B 259 MET cc_start: 0.0420 (ppp) cc_final: -0.0013 (ppp) REVERT: C 356 ILE cc_start: 0.3844 (mm) cc_final: 0.3561 (mm) REVERT: F 256 ASP cc_start: 0.1587 (t0) cc_final: 0.0861 (m-30) REVERT: F 365 LYS cc_start: 0.1762 (ptmt) cc_final: 0.1176 (ttpp) REVERT: F 576 LYS cc_start: 0.1575 (mmmt) cc_final: 0.0095 (mttt) REVERT: a 52 ARG cc_start: 0.7465 (mmt90) cc_final: 0.6772 (mtp85) REVERT: c 90 ASP cc_start: 0.6952 (t0) cc_final: 0.5832 (t0) REVERT: c 92 GLU cc_start: 0.6277 (pm20) cc_final: 0.5904 (pm20) REVERT: c 93 LEU cc_start: 0.8567 (mm) cc_final: 0.8176 (mm) REVERT: d 59 MET cc_start: 0.8631 (ptm) cc_final: 0.8343 (ptp) REVERT: e 60 LEU cc_start: 0.7434 (mt) cc_final: 0.6882 (pp) REVERT: e 105 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7613 (tm-30) REVERT: g 56 GLU cc_start: 0.8912 (mp0) cc_final: 0.8506 (mp0) REVERT: g 91 GLU cc_start: 0.8625 (pm20) cc_final: 0.7975 (mp0) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.3894 time to fit residues: 119.2316 Evaluate side-chains 152 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 0.0470 chunk 274 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 130 optimal weight: 0.0270 chunk 190 optimal weight: 0.9990 chunk 287 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS E 444 GLN ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN B 38 HIS ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN a 108 ASN f 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4727 moved from start: 0.8860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.204 29033 Z= 0.466 Angle : 0.611 24.063 40447 Z= 0.348 Chirality : 0.038 0.215 4466 Planarity : 0.004 0.057 4129 Dihedral : 26.264 88.776 6239 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.05 % Rotamer: Outliers : 0.04 % Allowed : 0.58 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2646 helix: 1.54 (0.13), residues: 1535 sheet: -0.93 (0.45), residues: 113 loop : -1.33 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 236 HIS 0.006 0.001 HIS E 448 PHE 0.018 0.001 PHE E 567 TYR 0.024 0.001 TYR F 372 ARG 0.007 0.000 ARG G 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1164 MET cc_start: 0.4687 (mtt) cc_final: 0.4361 (mtm) REVERT: A 1257 MET cc_start: 0.2055 (mtp) cc_final: 0.1436 (ppp) REVERT: E 258 GLU cc_start: 0.1947 (tp30) cc_final: 0.0423 (mp0) REVERT: E 564 ARG cc_start: 0.4749 (mtp85) cc_final: 0.3844 (mpt180) REVERT: B 38 HIS cc_start: 0.3962 (OUTLIER) cc_final: 0.3159 (m170) REVERT: B 259 MET cc_start: 0.0500 (ppp) cc_final: 0.0068 (ppp) REVERT: C 311 LYS cc_start: 0.0329 (mttt) cc_final: -0.0527 (tptm) REVERT: F 256 ASP cc_start: 0.1253 (t0) cc_final: 0.0491 (m-30) REVERT: F 365 LYS cc_start: 0.1821 (ptmt) cc_final: 0.1203 (ttpp) REVERT: F 576 LYS cc_start: 0.1589 (mmmt) cc_final: 0.0087 (mttt) REVERT: a 52 ARG cc_start: 0.7430 (mmt90) cc_final: 0.6738 (mtp85) REVERT: b 59 LYS cc_start: 0.8644 (ptmt) cc_final: 0.8352 (pttm) REVERT: c 90 ASP cc_start: 0.6924 (t0) cc_final: 0.6159 (t0) REVERT: c 93 LEU cc_start: 0.8646 (mm) cc_final: 0.8317 (mm) REVERT: e 60 LEU cc_start: 0.7215 (mt) cc_final: 0.6645 (pp) REVERT: e 105 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7630 (tm-30) REVERT: g 91 GLU cc_start: 0.8572 (pm20) cc_final: 0.7947 (mp0) REVERT: G 107 MET cc_start: 0.6401 (ttm) cc_final: 0.6106 (ttp) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3775 time to fit residues: 108.8429 Evaluate side-chains 147 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 9.9990 chunk 244 optimal weight: 0.1980 chunk 70 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 63 optimal weight: 30.0000 chunk 229 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 HIS ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.082301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.057376 restraints weight = 269353.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.058941 restraints weight = 153751.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.059940 restraints weight = 106173.280| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.9041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.203 29033 Z= 0.465 Angle : 0.603 24.111 40447 Z= 0.345 Chirality : 0.038 0.265 4466 Planarity : 0.004 0.056 4129 Dihedral : 26.212 89.855 6239 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2646 helix: 1.52 (0.13), residues: 1542 sheet: -1.02 (0.45), residues: 113 loop : -1.35 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 236 HIS 0.006 0.001 HIS E 448 PHE 0.017 0.001 PHE E 567 TYR 0.024 0.001 TYR F 372 ARG 0.005 0.000 ARG G 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.41 seconds wall clock time: 102 minutes 20.92 seconds (6140.92 seconds total)