Starting phenix.real_space_refine on Mon Jun 24 19:41:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/06_2024/8ouw_17204_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/06_2024/8ouw_17204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/06_2024/8ouw_17204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/06_2024/8ouw_17204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/06_2024/8ouw_17204_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/06_2024/8ouw_17204_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 79 5.49 5 Mg 4 5.21 5 S 330 5.16 5 C 33611 2.51 5 N 9396 2.21 5 O 10329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 151": "NH1" <-> "NH2" Residue "2 ARG 153": "NH1" <-> "NH2" Residue "2 ARG 156": "NH1" <-> "NH2" Residue "2 ARG 170": "NH1" <-> "NH2" Residue "2 ARG 171": "NH1" <-> "NH2" Residue "2 ARG 177": "NH1" <-> "NH2" Residue "2 ARG 201": "NH1" <-> "NH2" Residue "2 ARG 237": "NH1" <-> "NH2" Residue "2 ARG 252": "NH1" <-> "NH2" Residue "2 ARG 260": "NH1" <-> "NH2" Residue "2 ARG 271": "NH1" <-> "NH2" Residue "2 ARG 274": "NH1" <-> "NH2" Residue "2 ARG 283": "NH1" <-> "NH2" Residue "2 ARG 324": "NH1" <-> "NH2" Residue "2 ARG 351": "NH1" <-> "NH2" Residue "2 ARG 365": "NH1" <-> "NH2" Residue "2 ARG 368": "NH1" <-> "NH2" Residue "2 ARG 440": "NH1" <-> "NH2" Residue "2 ARG 451": "NH1" <-> "NH2" Residue "2 ARG 468": "NH1" <-> "NH2" Residue "2 ARG 476": "NH1" <-> "NH2" Residue "2 ARG 489": "NH1" <-> "NH2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 ARG 517": "NH1" <-> "NH2" Residue "2 ARG 572": "NH1" <-> "NH2" Residue "2 ARG 598": "NH1" <-> "NH2" Residue "2 ARG 611": "NH1" <-> "NH2" Residue "2 TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 616": "NH1" <-> "NH2" Residue "2 ARG 631": "NH1" <-> "NH2" Residue "2 ARG 639": "NH1" <-> "NH2" Residue "2 ARG 649": "NH1" <-> "NH2" Residue "2 ARG 659": "NH1" <-> "NH2" Residue "2 ARG 683": "NH1" <-> "NH2" Residue "2 ARG 687": "NH1" <-> "NH2" Residue "2 ARG 695": "NH1" <-> "NH2" Residue "2 ARG 702": "NH1" <-> "NH2" Residue "2 ARG 725": "NH1" <-> "NH2" Residue "2 ARG 739": "NH1" <-> "NH2" Residue "2 ARG 746": "NH1" <-> "NH2" Residue "2 ARG 757": "NH1" <-> "NH2" Residue "2 ARG 770": "NH1" <-> "NH2" Residue "2 ARG 786": "NH1" <-> "NH2" Residue "2 ARG 794": "NH1" <-> "NH2" Residue "2 ARG 800": "NH1" <-> "NH2" Residue "2 ARG 815": "NH1" <-> "NH2" Residue "2 ARG 824": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 17": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "3 ARG 61": "NH1" <-> "NH2" Residue "3 ARG 67": "NH1" <-> "NH2" Residue "3 ARG 92": "NH1" <-> "NH2" Residue "3 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 114": "NH1" <-> "NH2" Residue "3 ARG 119": "NH1" <-> "NH2" Residue "3 ARG 143": "NH1" <-> "NH2" Residue "3 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 220": "NH1" <-> "NH2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 239": "NH1" <-> "NH2" Residue "3 ARG 241": "NH1" <-> "NH2" Residue "3 ARG 247": "NH1" <-> "NH2" Residue "3 ARG 262": "NH1" <-> "NH2" Residue "3 ARG 290": "NH1" <-> "NH2" Residue "3 ARG 296": "NH1" <-> "NH2" Residue "3 ARG 304": "NH1" <-> "NH2" Residue "3 ARG 337": "NH1" <-> "NH2" Residue "3 ARG 339": "NH1" <-> "NH2" Residue "3 ARG 359": "NH1" <-> "NH2" Residue "3 ARG 363": "NH1" <-> "NH2" Residue "3 ARG 367": "NH1" <-> "NH2" Residue "3 ARG 374": "NH1" <-> "NH2" Residue "3 ARG 394": "NH1" <-> "NH2" Residue "3 ARG 395": "NH1" <-> "NH2" Residue "3 ARG 406": "NH1" <-> "NH2" Residue "3 ARG 422": "NH1" <-> "NH2" Residue "3 ARG 433": "NH1" <-> "NH2" Residue "3 ARG 448": "NH1" <-> "NH2" Residue "3 ARG 461": "NH1" <-> "NH2" Residue "3 ARG 481": "NH1" <-> "NH2" Residue "3 ARG 511": "NH1" <-> "NH2" Residue "3 ARG 566": "NH1" <-> "NH2" Residue "3 ARG 573": "NH1" <-> "NH2" Residue "3 ARG 595": "NH1" <-> "NH2" Residue "3 ARG 606": "NH1" <-> "NH2" Residue "3 ARG 613": "NH1" <-> "NH2" Residue "3 ARG 620": "NH1" <-> "NH2" Residue "3 ARG 629": "NH1" <-> "NH2" Residue "3 ARG 636": "NH1" <-> "NH2" Residue "3 ARG 658": "NH1" <-> "NH2" Residue "4 ARG 104": "NH1" <-> "NH2" Residue "4 ARG 111": "NH1" <-> "NH2" Residue "4 ARG 119": "NH1" <-> "NH2" Residue "4 ARG 122": "NH1" <-> "NH2" Residue "4 ARG 160": "NH1" <-> "NH2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 ARG 212": "NH1" <-> "NH2" Residue "4 ARG 215": "NH1" <-> "NH2" Residue "4 ARG 224": "NH1" <-> "NH2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 235": "NH1" <-> "NH2" Residue "4 ARG 254": "NH1" <-> "NH2" Residue "4 ARG 263": "NH1" <-> "NH2" Residue "4 ARG 284": "NH1" <-> "NH2" Residue "4 ARG 306": "NH1" <-> "NH2" Residue "4 ARG 350": "NH1" <-> "NH2" Residue "4 ARG 358": "NH1" <-> "NH2" Residue "4 ARG 369": "NH1" <-> "NH2" Residue "4 ARG 376": "NH1" <-> "NH2" Residue "4 ARG 385": "NH1" <-> "NH2" Residue "4 ARG 391": "NH1" <-> "NH2" Residue "4 ARG 404": "NH1" <-> "NH2" Residue "4 ARG 414": "NH1" <-> "NH2" Residue "4 ARG 437": "NH1" <-> "NH2" Residue "4 ARG 448": "NH1" <-> "NH2" Residue "4 ARG 460": "NH1" <-> "NH2" Residue "4 ARG 484": "NH1" <-> "NH2" Residue "4 ARG 488": "NH1" <-> "NH2" Residue "4 ARG 508": "NH1" <-> "NH2" Residue "4 ARG 543": "NH1" <-> "NH2" Residue "4 ARG 569": "NH1" <-> "NH2" Residue "4 ARG 585": "NH1" <-> "NH2" Residue "4 ARG 602": "NH1" <-> "NH2" Residue "4 ARG 619": "NH1" <-> "NH2" Residue "4 ARG 620": "NH1" <-> "NH2" Residue "4 ARG 648": "NH1" <-> "NH2" Residue "4 ARG 678": "NH1" <-> "NH2" Residue "4 ARG 692": "NH1" <-> "NH2" Residue "4 ARG 699": "NH1" <-> "NH2" Residue "4 ARG 708": "NH1" <-> "NH2" Residue "4 ARG 726": "NH1" <-> "NH2" Residue "5 ARG 26": "NH1" <-> "NH2" Residue "5 ARG 33": "NH1" <-> "NH2" Residue "5 ARG 40": "NH1" <-> "NH2" Residue "5 ARG 44": "NH1" <-> "NH2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 61": "NH1" <-> "NH2" Residue "5 ARG 69": "NH1" <-> "NH2" Residue "5 ARG 89": "NH1" <-> "NH2" Residue "5 ARG 114": "NH1" <-> "NH2" Residue "5 ARG 138": "NH1" <-> "NH2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 ARG 173": "NH1" <-> "NH2" Residue "5 ARG 195": "NH1" <-> "NH2" Residue "5 ARG 244": "NH1" <-> "NH2" Residue "5 ARG 252": "NH1" <-> "NH2" Residue "5 ARG 263": "NH1" <-> "NH2" Residue "5 ARG 289": "NH1" <-> "NH2" Residue "5 ARG 294": "NH1" <-> "NH2" Residue "5 ARG 319": "NH1" <-> "NH2" Residue "5 ARG 327": "NH1" <-> "NH2" Residue "5 ARG 361": "NH1" <-> "NH2" Residue "5 ARG 370": "NH1" <-> "NH2" Residue "5 ARG 371": "NH1" <-> "NH2" Residue "5 ARG 480": "NH1" <-> "NH2" Residue "5 ARG 512": "NH1" <-> "NH2" Residue "5 ARG 587": "NH1" <-> "NH2" Residue "5 ARG 593": "NH1" <-> "NH2" Residue "5 ARG 610": "NH1" <-> "NH2" Residue "5 ARG 635": "NH1" <-> "NH2" Residue "5 ARG 642": "NH1" <-> "NH2" Residue "5 ARG 666": "NH1" <-> "NH2" Residue "5 ARG 669": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 79": "NH1" <-> "NH2" Residue "6 ARG 101": "NH1" <-> "NH2" Residue "6 ARG 123": "NH1" <-> "NH2" Residue "6 ARG 135": "NH1" <-> "NH2" Residue "6 ARG 142": "NH1" <-> "NH2" Residue "6 ARG 152": "NH1" <-> "NH2" Residue "6 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 165": "NH1" <-> "NH2" Residue "6 ARG 172": "NH1" <-> "NH2" Residue "6 ARG 187": "NH1" <-> "NH2" Residue "6 ARG 189": "NH1" <-> "NH2" Residue "6 ARG 206": "NH1" <-> "NH2" Residue "6 ARG 216": "NH1" <-> "NH2" Residue "6 ARG 221": "NH1" <-> "NH2" Residue "6 ARG 228": "NH1" <-> "NH2" Residue "6 ARG 262": "NH1" <-> "NH2" Residue "6 ARG 289": "NH1" <-> "NH2" Residue "6 ARG 334": "NH1" <-> "NH2" Residue "6 ARG 381": "NH1" <-> "NH2" Residue "6 ARG 388": "NH1" <-> "NH2" Residue "6 ARG 416": "NH1" <-> "NH2" Residue "6 ARG 497": "NH1" <-> "NH2" Residue "6 ARG 510": "NH1" <-> "NH2" Residue "6 ARG 513": "NH1" <-> "NH2" Residue "6 ARG 515": "NH1" <-> "NH2" Residue "6 ARG 530": "NH1" <-> "NH2" Residue "6 ARG 551": "NH1" <-> "NH2" Residue "6 ARG 552": "NH1" <-> "NH2" Residue "6 ARG 558": "NH1" <-> "NH2" Residue "6 ARG 566": "NH1" <-> "NH2" Residue "6 ARG 583": "NH1" <-> "NH2" Residue "6 ARG 599": "NH1" <-> "NH2" Residue "6 ARG 605": "NH1" <-> "NH2" Residue "6 ARG 618": "NH1" <-> "NH2" Residue "6 ARG 622": "NH1" <-> "NH2" Residue "6 ARG 629": "NH1" <-> "NH2" Residue "6 ARG 636": "NH1" <-> "NH2" Residue "6 ARG 661": "NH1" <-> "NH2" Residue "6 ARG 730": "NH1" <-> "NH2" Residue "6 ARG 776": "NH1" <-> "NH2" Residue "6 ARG 780": "NH1" <-> "NH2" Residue "7 ARG 18": "NH1" <-> "NH2" Residue "7 ARG 39": "NH1" <-> "NH2" Residue "7 ARG 47": "NH1" <-> "NH2" Residue "7 ARG 48": "NH1" <-> "NH2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 ARG 116": "NH1" <-> "NH2" Residue "7 ARG 121": "NH1" <-> "NH2" Residue "7 ARG 136": "NH1" <-> "NH2" Residue "7 ARG 146": "NH1" <-> "NH2" Residue "7 ARG 163": "NH1" <-> "NH2" Residue "7 ARG 182": "NH1" <-> "NH2" Residue "7 ARG 232": "NH1" <-> "NH2" Residue "7 ARG 238": "NH1" <-> "NH2" Residue "7 ARG 264": "NH1" <-> "NH2" Residue "7 ARG 276": "NH1" <-> "NH2" Residue "7 ARG 336": "NH1" <-> "NH2" Residue "7 ARG 337": "NH1" <-> "NH2" Residue "7 ARG 381": "NH1" <-> "NH2" Residue "7 ARG 405": "NH1" <-> "NH2" Residue "7 ARG 409": "NH1" <-> "NH2" Residue "7 ARG 416": "NH1" <-> "NH2" Residue "7 ARG 464": "NH1" <-> "NH2" Residue "7 ARG 490": "NH1" <-> "NH2" Residue "7 ARG 503": "NH1" <-> "NH2" Residue "7 ARG 508": "NH1" <-> "NH2" Residue "7 ARG 523": "NH1" <-> "NH2" Residue "7 ARG 536": "NH1" <-> "NH2" Residue "7 ARG 558": "NH1" <-> "NH2" Residue "7 ARG 570": "NH1" <-> "NH2" Residue "7 ARG 588": "NH1" <-> "NH2" Residue "7 ARG 590": "NH1" <-> "NH2" Residue "7 ARG 599": "NH1" <-> "NH2" Residue "7 ARG 600": "NH1" <-> "NH2" Residue "7 ARG 603": "NH1" <-> "NH2" Residue "7 ARG 614": "NH1" <-> "NH2" Residue "7 ARG 621": "NH1" <-> "NH2" Residue "7 ARG 626": "NH1" <-> "NH2" Residue "7 ARG 630": "NH1" <-> "NH2" Residue "7 ARG 645": "NH1" <-> "NH2" Residue "7 ARG 655": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 183": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "E ARG 391": "NH1" <-> "NH2" Residue "E ARG 393": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 464": "NH1" <-> "NH2" Residue "E ARG 476": "NH1" <-> "NH2" Residue "E ARG 485": "NH1" <-> "NH2" Residue "E ARG 527": "NH1" <-> "NH2" Residue "E ARG 531": "NH1" <-> "NH2" Residue "E ARG 540": "NH1" <-> "NH2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ARG 558": "NH1" <-> "NH2" Residue "E ARG 560": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 176": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F ARG 282": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 563": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 176": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 241": "NH1" <-> "NH2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "G ARG 282": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 544": "NH1" <-> "NH2" Residue "G ARG 563": "NH1" <-> "NH2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 35": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K ARG 93": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K ARG 132": "NH1" <-> "NH2" Residue "K ARG 145": "NH1" <-> "NH2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K ARG 150": "NH1" <-> "NH2" Residue "K ARG 155": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 175": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K ARG 207": "NH1" <-> "NH2" Residue "K ARG 251": "NH1" <-> "NH2" Residue "K ARG 265": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "K ARG 307": "NH1" <-> "NH2" Residue "K ARG 312": "NH1" <-> "NH2" Residue "K ARG 315": "NH1" <-> "NH2" Residue "K ARG 317": "NH1" <-> "NH2" Residue "K ARG 318": "NH1" <-> "NH2" Residue "K ARG 334": "NH1" <-> "NH2" Residue "K ARG 338": "NH1" <-> "NH2" Residue "K ARG 343": "NH1" <-> "NH2" Residue "K ARG 351": "NH1" <-> "NH2" Residue "K TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 381": "NH1" <-> "NH2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "K ARG 387": "NH1" <-> "NH2" Residue "K ARG 394": "NH1" <-> "NH2" Residue "K ARG 448": "NH1" <-> "NH2" Residue "K ARG 460": "NH1" <-> "NH2" Residue "K ARG 465": "NH1" <-> "NH2" Residue "K ARG 477": "NH1" <-> "NH2" Residue "K PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 498": "NH1" <-> "NH2" Residue "K ARG 513": "NH1" <-> "NH2" Residue "K ARG 877": "NH1" <-> "NH2" Residue "K ARG 912": "NH1" <-> "NH2" Residue "K ARG 916": "NH1" <-> "NH2" Residue "K PHE 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 950": "NH1" <-> "NH2" Residue "L ARG 52": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "L ARG 121": "NH1" <-> "NH2" Residue "L ARG 122": "NH1" <-> "NH2" Residue "L ARG 132": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 53754 Number of models: 1 Model: "" Number of chains: 25 Chain: "2" Number of atoms: 5547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5547 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 671} Chain breaks: 7 Chain: "3" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4872 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 23, 'TRANS': 595} Chain breaks: 3 Chain: "4" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4906 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 21, 'TRANS': 597} Chain breaks: 2 Chain: "5" Number of atoms: 4256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4256 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 514} Chain breaks: 9 Chain: "6" Number of atoms: 5595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5595 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 19, 'TRANS': 687} Chain breaks: 5 Chain: "7" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4963 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 26, 'TRANS': 605} Chain breaks: 3 Chain: "A" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1534 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1423 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1404 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "D" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1625 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 192} Chain: "E" Number of atoms: 4547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4547 Classifications: {'peptide': 563} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 543} Chain breaks: 1 Chain: "F" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2741 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 326} Chain breaks: 3 Chain: "G" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2564 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 306} Chain breaks: 2 Chain: "H" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 148 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 611 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "K" Number of atoms: 5446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5446 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 13, 'TRANS': 642} Chain breaks: 1 Chain: "L" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 681 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "M" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 578 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1410 SG CYS 2 305 112.452 122.683 106.619 1.00 88.05 S ATOM 1428 SG CYS 2 308 115.665 123.827 105.068 1.00 84.48 S ATOM 1587 SG CYS 2 328 114.133 125.625 107.991 1.00 84.41 S ATOM 1606 SG CYS 2 331 112.710 126.225 104.616 1.00 83.18 S ATOM 11771 SG CYS 4 269 79.092 148.202 123.311 1.00 89.97 S ATOM 11789 SG CYS 4 272 78.830 151.836 124.444 1.00 89.01 S ATOM 11933 SG CYS 4 291 76.783 150.508 121.444 1.00 85.09 S ATOM 11954 SG CYS 4 294 80.424 151.259 121.170 1.00 84.30 S ATOM 16531 SG CYS 5 172 93.368 112.682 93.360 1.00 84.67 S ATOM 16557 SG CYS 5 175 94.160 113.654 89.817 1.00 78.19 S ATOM 16723 SG CYS 5 197 96.363 114.983 92.443 1.00 77.52 S ATOM 16739 SG CYS 5 208 92.779 116.284 92.352 1.00 69.16 S ATOM 20855 SG CYS 6 157 96.547 141.931 119.586 1.00 87.90 S ATOM 20878 SG CYS 6 160 98.644 144.961 119.864 1.00 81.89 S ATOM 21035 SG CYS 6 179 94.870 145.144 120.528 1.00 79.00 S ATOM 21070 SG CYS 6 184 96.097 144.817 116.969 1.00 78.30 S ATOM 26678 SG CYS 7 197 60.009 136.556 103.125 1.00 88.61 S ATOM 26699 SG CYS 7 200 58.770 137.555 99.839 1.00 83.23 S ATOM 26843 SG CYS 7 219 61.360 134.868 100.198 1.00 81.22 S ATOM 26882 SG CYS 7 224 62.473 138.513 100.619 1.00 79.40 S Time building chain proxies: 20.43, per 1000 atoms: 0.38 Number of scatterers: 53754 At special positions: 0 Unit cell: (216.265, 217.56, 222.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 330 16.00 P 79 15.00 Mg 4 11.99 O 10329 8.00 N 9396 7.00 C 33611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.01 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 328 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 308 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 305 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 331 " pdb=" ZN 41503 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 272 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 291 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 294 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 269 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 197 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 208 " pdb=" ZN 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 179 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 160 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 157 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 184 " pdb=" ZN 71502 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 219 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 200 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 197 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 224 " Number of angles added : 30 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 291 helices and 59 sheets defined 45.3% alpha, 13.7% beta 29 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 18.17 Creating SS restraints... Processing helix chain '2' and resid 101 through 105 Processing helix chain '2' and resid 108 through 110 No H-bonds generated for 'chain '2' and resid 108 through 110' Processing helix chain '2' and resid 147 through 150 Processing helix chain '2' and resid 155 through 157 No H-bonds generated for 'chain '2' and resid 155 through 157' Processing helix chain '2' and resid 162 through 178 removed outlier: 3.644A pdb=" N GLU 2 167 " --> pdb=" O ALA 2 163 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS 2 173 " --> pdb=" O GLU 2 169 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 199 removed outlier: 3.620A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 212 Processing helix chain '2' and resid 218 through 224 Processing helix chain '2' and resid 228 through 246 removed outlier: 4.034A pdb=" N ALA 2 233 " --> pdb=" O ASN 2 229 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE 2 234 " --> pdb=" O GLU 2 230 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN 2 245 " --> pdb=" O GLU 2 241 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET 2 246 " --> pdb=" O VAL 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 248 through 251 removed outlier: 3.987A pdb=" N SER 2 251 " --> pdb=" O PRO 2 248 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 248 through 251' Processing helix chain '2' and resid 270 through 272 No H-bonds generated for 'chain '2' and resid 270 through 272' Processing helix chain '2' and resid 275 through 277 No H-bonds generated for 'chain '2' and resid 275 through 277' Processing helix chain '2' and resid 358 through 360 No H-bonds generated for 'chain '2' and resid 358 through 360' Processing helix chain '2' and resid 376 through 378 No H-bonds generated for 'chain '2' and resid 376 through 378' Processing helix chain '2' and resid 400 through 406 Processing helix chain '2' and resid 433 through 443 Processing helix chain '2' and resid 448 through 455 Processing helix chain '2' and resid 464 through 474 Processing helix chain '2' and resid 504 through 514 removed outlier: 4.189A pdb=" N LEU 2 508 " --> pdb=" O LYS 2 504 " (cutoff:3.500A) Processing helix chain '2' and resid 550 through 553 No H-bonds generated for 'chain '2' and resid 550 through 553' Processing helix chain '2' and resid 564 through 566 No H-bonds generated for 'chain '2' and resid 564 through 566' Processing helix chain '2' and resid 569 through 581 Processing helix chain '2' and resid 608 through 610 No H-bonds generated for 'chain '2' and resid 608 through 610' Processing helix chain '2' and resid 618 through 621 No H-bonds generated for 'chain '2' and resid 618 through 621' Processing helix chain '2' and resid 626 through 631 removed outlier: 4.554A pdb=" N ARG 2 631 " --> pdb=" O PRO 2 627 " (cutoff:3.500A) Processing helix chain '2' and resid 644 through 661 Processing helix chain '2' and resid 691 through 703 removed outlier: 3.631A pdb=" N GLU 2 703 " --> pdb=" O ILE 2 699 " (cutoff:3.500A) Processing helix chain '2' and resid 711 through 731 removed outlier: 4.130A pdb=" N SER 2 718 " --> pdb=" O GLU 2 715 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN 2 719 " --> pdb=" O LYS 2 716 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE 2 720 " --> pdb=" O PHE 2 717 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG 2 725 " --> pdb=" O ALA 2 722 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET 2 729 " --> pdb=" O LYS 2 726 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 2 730 " --> pdb=" O GLU 2 727 " (cutoff:3.500A) Processing helix chain '2' and resid 738 through 754 Processing helix chain '2' and resid 762 through 779 removed outlier: 3.800A pdb=" N ASN 2 778 " --> pdb=" O GLU 2 774 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR 2 779 " --> pdb=" O SER 2 775 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 791 Processing helix chain '2' and resid 793 through 796 No H-bonds generated for 'chain '2' and resid 793 through 796' Processing helix chain '2' and resid 802 through 823 Processing helix chain '2' and resid 838 through 846 Processing helix chain '2' and resid 856 through 858 No H-bonds generated for 'chain '2' and resid 856 through 858' Processing helix chain '2' and resid 860 through 864 Processing helix chain '3' and resid 12 through 29 Processing helix chain '3' and resid 38 through 48 Processing helix chain '3' and resid 57 through 63 removed outlier: 3.540A pdb=" N GLU 3 62 " --> pdb=" O ASP 3 58 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE 3 63 " --> pdb=" O GLU 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 65 through 68 No H-bonds generated for 'chain '3' and resid 65 through 68' Processing helix chain '3' and resid 70 through 73 No H-bonds generated for 'chain '3' and resid 70 through 73' Processing helix chain '3' and resid 75 through 91 Processing helix chain '3' and resid 112 through 114 No H-bonds generated for 'chain '3' and resid 112 through 114' Processing helix chain '3' and resid 123 through 125 No H-bonds generated for 'chain '3' and resid 123 through 125' Processing helix chain '3' and resid 228 through 230 No H-bonds generated for 'chain '3' and resid 228 through 230' Processing helix chain '3' and resid 283 through 294 Processing helix chain '3' and resid 298 through 305 Processing helix chain '3' and resid 314 through 325 Processing helix chain '3' and resid 354 through 364 Processing helix chain '3' and resid 378 through 382 Processing helix chain '3' and resid 400 through 403 No H-bonds generated for 'chain '3' and resid 400 through 403' Processing helix chain '3' and resid 414 through 416 No H-bonds generated for 'chain '3' and resid 414 through 416' Processing helix chain '3' and resid 419 through 424 removed outlier: 4.022A pdb=" N ALA 3 424 " --> pdb=" O ILE 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 426 through 431 removed outlier: 3.801A pdb=" N GLU 3 430 " --> pdb=" O HIS 3 426 " (cutoff:3.500A) Processing helix chain '3' and resid 468 through 472 Processing helix chain '3' and resid 476 through 481 removed outlier: 4.115A pdb=" N ARG 3 481 " --> pdb=" O SER 3 477 " (cutoff:3.500A) Processing helix chain '3' and resid 494 through 508 Processing helix chain '3' and resid 562 through 574 removed outlier: 4.352A pdb=" N SER 3 574 " --> pdb=" O HIS 3 570 " (cutoff:3.500A) Processing helix chain '3' and resid 581 through 596 removed outlier: 3.665A pdb=" N ALA 3 592 " --> pdb=" O SER 3 588 " (cutoff:3.500A) Processing helix chain '3' and resid 599 through 601 No H-bonds generated for 'chain '3' and resid 599 through 601' Processing helix chain '3' and resid 612 through 628 removed outlier: 3.696A pdb=" N GLU 3 616 " --> pdb=" O ALA 3 612 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA 3 628 " --> pdb=" O ALA 3 624 " (cutoff:3.500A) Processing helix chain '3' and resid 636 through 650 removed outlier: 3.798A pdb=" N LYS 3 641 " --> pdb=" O GLU 3 637 " (cutoff:3.500A) Processing helix chain '4' and resid 114 through 127 removed outlier: 3.503A pdb=" N GLN 4 118 " --> pdb=" O VAL 4 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER 4 120 " --> pdb=" O ASP 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 130 through 134 removed outlier: 4.361A pdb=" N LEU 4 133 " --> pdb=" O ILE 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 156 through 166 removed outlier: 3.868A pdb=" N LEU 4 162 " --> pdb=" O MET 4 158 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU 4 163 " --> pdb=" O GLU 4 159 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS 4 164 " --> pdb=" O ARG 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 176 through 182 Processing helix chain '4' and resid 184 through 192 removed outlier: 4.072A pdb=" N LYS 4 189 " --> pdb=" O ALA 4 185 " (cutoff:3.500A) Processing helix chain '4' and resid 194 through 213 removed outlier: 3.662A pdb=" N ILE 4 198 " --> pdb=" O PRO 4 194 " (cutoff:3.500A) Proline residue: 4 199 - end of helix removed outlier: 3.551A pdb=" N ASP 4 202 " --> pdb=" O ILE 4 198 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE 4 203 " --> pdb=" O PRO 4 199 " (cutoff:3.500A) Processing helix chain '4' and resid 234 through 236 No H-bonds generated for 'chain '4' and resid 234 through 236' Processing helix chain '4' and resid 239 through 241 No H-bonds generated for 'chain '4' and resid 239 through 241' Processing helix chain '4' and resid 339 through 341 No H-bonds generated for 'chain '4' and resid 339 through 341' Processing helix chain '4' and resid 402 through 413 removed outlier: 3.934A pdb=" N LYS 4 413 " --> pdb=" O ILE 4 409 " (cutoff:3.500A) Processing helix chain '4' and resid 417 through 424 removed outlier: 3.680A pdb=" N SER 4 424 " --> pdb=" O ALA 4 420 " (cutoff:3.500A) Processing helix chain '4' and resid 433 through 444 Processing helix chain '4' and resid 475 through 485 Processing helix chain '4' and resid 494 through 496 No H-bonds generated for 'chain '4' and resid 494 through 496' Processing helix chain '4' and resid 499 through 503 removed outlier: 3.707A pdb=" N THR 4 503 " --> pdb=" O ALA 4 499 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 499 through 503' Processing helix chain '4' and resid 521 through 524 No H-bonds generated for 'chain '4' and resid 521 through 524' Processing helix chain '4' and resid 535 through 537 No H-bonds generated for 'chain '4' and resid 535 through 537' Processing helix chain '4' and resid 540 through 552 removed outlier: 4.075A pdb=" N VAL 4 545 " --> pdb=" O SER 4 541 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU 4 546 " --> pdb=" O ALA 4 542 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N HIS 4 547 " --> pdb=" O ARG 4 543 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU 4 548 " --> pdb=" O SER 4 544 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL 4 549 " --> pdb=" O VAL 4 545 " (cutoff:3.500A) Processing helix chain '4' and resid 589 through 592 No H-bonds generated for 'chain '4' and resid 589 through 592' Processing helix chain '4' and resid 597 through 602 removed outlier: 4.192A pdb=" N ARG 4 602 " --> pdb=" O THR 4 598 " (cutoff:3.500A) Processing helix chain '4' and resid 615 through 629 removed outlier: 3.764A pdb=" N LEU 4 628 " --> pdb=" O HIS 4 624 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR 4 629 " --> pdb=" O LEU 4 625 " (cutoff:3.500A) Processing helix chain '4' and resid 644 through 657 removed outlier: 3.761A pdb=" N ASP 4 649 " --> pdb=" O ASN 4 645 " (cutoff:3.500A) Processing helix chain '4' and resid 664 through 682 removed outlier: 3.817A pdb=" N ALA 4 682 " --> pdb=" O ARG 4 678 " (cutoff:3.500A) Processing helix chain '4' and resid 691 through 707 Processing helix chain '4' and resid 715 through 729 removed outlier: 3.799A pdb=" N LEU 4 729 " --> pdb=" O TRP 4 725 " (cutoff:3.500A) Processing helix chain '5' and resid 25 through 45 Processing helix chain '5' and resid 54 through 64 Processing helix chain '5' and resid 74 through 80 Processing helix chain '5' and resid 82 through 90 Processing helix chain '5' and resid 92 through 111 Proline residue: 5 97 - end of helix Processing helix chain '5' and resid 142 through 144 No H-bonds generated for 'chain '5' and resid 142 through 144' Processing helix chain '5' and resid 252 through 254 No H-bonds generated for 'chain '5' and resid 252 through 254' Processing helix chain '5' and resid 315 through 326 Processing helix chain '5' and resid 330 through 337 Processing helix chain '5' and resid 346 through 357 Processing helix chain '5' and resid 386 through 396 Processing helix chain '5' and resid 432 through 434 No H-bonds generated for 'chain '5' and resid 432 through 434' Processing helix chain '5' and resid 458 through 463 Processing helix chain '5' and resid 509 through 512 Processing helix chain '5' and resid 525 through 546 removed outlier: 3.863A pdb=" N THR 5 530 " --> pdb=" O LEU 5 526 " (cutoff:3.500A) Processing helix chain '5' and resid 576 through 587 removed outlier: 3.799A pdb=" N LYS 5 581 " --> pdb=" O GLU 5 577 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 610 removed outlier: 3.901A pdb=" N LYS 5 601 " --> pdb=" O GLN 5 597 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU 5 602 " --> pdb=" O ALA 5 598 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL 5 603 " --> pdb=" O SER 5 599 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN 5 604 " --> pdb=" O GLU 5 600 " (cutoff:3.500A) Processing helix chain '5' and resid 634 through 650 removed outlier: 3.664A pdb=" N MET 5 650 " --> pdb=" O SER 5 646 " (cutoff:3.500A) Processing helix chain '5' and resid 658 through 677 removed outlier: 4.378A pdb=" N GLU 5 674 " --> pdb=" O VAL 5 670 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA 5 675 " --> pdb=" O SER 5 671 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA 5 676 " --> pdb=" O THR 5 672 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 5 No H-bonds generated for 'chain '6' and resid 2 through 5' Processing helix chain '6' and resid 15 through 30 Processing helix chain '6' and resid 39 through 48 removed outlier: 4.201A pdb=" N LYS 6 45 " --> pdb=" O LYS 6 41 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU 6 46 " --> pdb=" O SER 6 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL 6 48 " --> pdb=" O MET 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 65 Processing helix chain '6' and resid 67 through 75 Processing helix chain '6' and resid 77 through 95 Proline residue: 6 82 - end of helix removed outlier: 3.659A pdb=" N ALA 6 95 " --> pdb=" O ALA 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 removed outlier: 4.069A pdb=" N GLN 6 102 " --> pdb=" O GLU 6 98 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN 6 103 " --> pdb=" O SER 6 99 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 124 No H-bonds generated for 'chain '6' and resid 122 through 124' Processing helix chain '6' and resid 127 through 129 No H-bonds generated for 'chain '6' and resid 127 through 129' Processing helix chain '6' and resid 211 through 213 No H-bonds generated for 'chain '6' and resid 211 through 213' Processing helix chain '6' and resid 229 through 231 No H-bonds generated for 'chain '6' and resid 229 through 231' Processing helix chain '6' and resid 253 through 255 No H-bonds generated for 'chain '6' and resid 253 through 255' Processing helix chain '6' and resid 264 through 267 No H-bonds generated for 'chain '6' and resid 264 through 267' Processing helix chain '6' and resid 323 through 328 Processing helix chain '6' and resid 332 through 342 Processing helix chain '6' and resid 346 through 354 removed outlier: 3.728A pdb=" N SER 6 353 " --> pdb=" O ASN 6 349 " (cutoff:3.500A) Processing helix chain '6' and resid 362 through 373 removed outlier: 3.534A pdb=" N LEU 6 373 " --> pdb=" O LEU 6 369 " (cutoff:3.500A) Processing helix chain '6' and resid 403 through 413 Processing helix chain '6' and resid 422 through 424 No H-bonds generated for 'chain '6' and resid 422 through 424' Processing helix chain '6' and resid 427 through 430 No H-bonds generated for 'chain '6' and resid 427 through 430' Processing helix chain '6' and resid 449 through 452 No H-bonds generated for 'chain '6' and resid 449 through 452' Processing helix chain '6' and resid 463 through 465 No H-bonds generated for 'chain '6' and resid 463 through 465' Processing helix chain '6' and resid 468 through 480 removed outlier: 3.731A pdb=" N GLN 6 480 " --> pdb=" O GLU 6 476 " (cutoff:3.500A) Processing helix chain '6' and resid 517 through 520 No H-bonds generated for 'chain '6' and resid 517 through 520' Processing helix chain '6' and resid 525 through 530 removed outlier: 3.807A pdb=" N ARG 6 530 " --> pdb=" O PRO 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 543 through 562 removed outlier: 3.551A pdb=" N GLU 6 562 " --> pdb=" O ARG 6 558 " (cutoff:3.500A) Processing helix chain '6' and resid 572 through 584 removed outlier: 3.674A pdb=" N ARG 6 583 " --> pdb=" O ILE 6 579 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N CYS 6 584 " --> pdb=" O ALA 6 580 " (cutoff:3.500A) Processing helix chain '6' and resid 591 through 610 Processing helix chain '6' and resid 621 through 637 Processing helix chain '6' and resid 645 through 659 Processing helix chain '6' and resid 716 through 734 removed outlier: 3.915A pdb=" N ASP 6 734 " --> pdb=" O ARG 6 730 " (cutoff:3.500A) Processing helix chain '6' and resid 746 through 755 Processing helix chain '6' and resid 769 through 783 Processing helix chain '7' and resid 10 through 23 Processing helix chain '7' and resid 37 through 46 Processing helix chain '7' and resid 57 through 61 Processing helix chain '7' and resid 68 through 77 Processing helix chain '7' and resid 79 through 98 removed outlier: 4.816A pdb=" N VAL 7 84 " --> pdb=" O LYS 7 80 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU 7 85 " --> pdb=" O ARG 7 81 " (cutoff:3.500A) Processing helix chain '7' and resid 108 through 121 removed outlier: 3.697A pdb=" N HIS 7 118 " --> pdb=" O PHE 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 133 through 138 Processing helix chain '7' and resid 141 through 144 No H-bonds generated for 'chain '7' and resid 141 through 144' Processing helix chain '7' and resid 156 through 158 No H-bonds generated for 'chain '7' and resid 156 through 158' Processing helix chain '7' and resid 167 through 169 No H-bonds generated for 'chain '7' and resid 167 through 169' Processing helix chain '7' and resid 222 through 227 Processing helix chain '7' and resid 254 through 256 No H-bonds generated for 'chain '7' and resid 254 through 256' Processing helix chain '7' and resid 272 through 274 No H-bonds generated for 'chain '7' and resid 272 through 274' Processing helix chain '7' and resid 330 through 338 removed outlier: 3.570A pdb=" N LEU 7 335 " --> pdb=" O GLU 7 331 " (cutoff:3.500A) Processing helix chain '7' and resid 342 through 347 Processing helix chain '7' and resid 357 through 366 Processing helix chain '7' and resid 375 through 377 No H-bonds generated for 'chain '7' and resid 375 through 377' Processing helix chain '7' and resid 396 through 406 Processing helix chain '7' and resid 420 through 423 No H-bonds generated for 'chain '7' and resid 420 through 423' Processing helix chain '7' and resid 442 through 445 No H-bonds generated for 'chain '7' and resid 442 through 445' Processing helix chain '7' and resid 456 through 458 No H-bonds generated for 'chain '7' and resid 456 through 458' Processing helix chain '7' and resid 461 through 473 removed outlier: 4.955A pdb=" N ALA 7 466 " --> pdb=" O HIS 7 462 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE 7 467 " --> pdb=" O ASP 7 463 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N HIS 7 468 " --> pdb=" O ARG 7 464 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU 7 469 " --> pdb=" O THR 7 465 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL 7 470 " --> pdb=" O ALA 7 466 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU 7 472 " --> pdb=" O HIS 7 468 " (cutoff:3.500A) Processing helix chain '7' and resid 510 through 513 No H-bonds generated for 'chain '7' and resid 510 through 513' Processing helix chain '7' and resid 518 through 523 removed outlier: 4.011A pdb=" N ARG 7 523 " --> pdb=" O ALA 7 519 " (cutoff:3.500A) Processing helix chain '7' and resid 536 through 552 removed outlier: 3.951A pdb=" N LYS 7 540 " --> pdb=" O ARG 7 536 " (cutoff:3.500A) Processing helix chain '7' and resid 566 through 578 removed outlier: 4.048A pdb=" N THR 7 578 " --> pdb=" O SER 7 574 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 603 removed outlier: 3.699A pdb=" N ARG 7 588 " --> pdb=" O PRO 7 585 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU 7 589 " --> pdb=" O ALA 7 586 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL 7 592 " --> pdb=" O GLU 7 589 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU 7 593 " --> pdb=" O ARG 7 590 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP 7 601 " --> pdb=" O MET 7 598 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA 7 602 " --> pdb=" O ARG 7 599 " (cutoff:3.500A) Processing helix chain '7' and resid 613 through 630 removed outlier: 3.716A pdb=" N ILE 7 616 " --> pdb=" O PRO 7 613 " (cutoff:3.500A) Processing helix chain '7' and resid 637 through 654 removed outlier: 4.050A pdb=" N LEU 7 654 " --> pdb=" O ALA 7 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 removed outlier: 4.069A pdb=" N GLN A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 60 Processing helix chain 'A' and resid 68 through 98 removed outlier: 4.174A pdb=" N PHE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 4.027A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 134 removed outlier: 4.048A pdb=" N ASN A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 5.033A pdb=" N MET A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 removed outlier: 4.167A pdb=" N ASN B 12 " --> pdb=" O PHE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 110 through 136 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 159 through 177 removed outlier: 3.804A pdb=" N ALA B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.002A pdb=" N SER C 67 " --> pdb=" O TRP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 138 through 146 removed outlier: 4.358A pdb=" N THR C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 179 removed outlier: 3.837A pdb=" N LYS C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN C 179 " --> pdb=" O THR C 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.734A pdb=" N ARG D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 67 Processing helix chain 'D' and resid 75 through 104 removed outlier: 3.863A pdb=" N SER D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 127 through 147 removed outlier: 4.005A pdb=" N LEU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 209 through 218 removed outlier: 5.269A pdb=" N GLN D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 10 No H-bonds generated for 'chain 'E' and resid 7 through 10' Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.665A pdb=" N HIS E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 68 removed outlier: 3.665A pdb=" N SER E 68 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 111 No H-bonds generated for 'chain 'E' and resid 108 through 111' Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.672A pdb=" N LEU E 129 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 159 through 190 Processing helix chain 'E' and resid 200 through 211 removed outlier: 3.567A pdb=" N ALA E 209 " --> pdb=" O GLU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 231 removed outlier: 3.726A pdb=" N ALA E 229 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 246 Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 288 through 294 removed outlier: 3.788A pdb=" N VAL E 294 " --> pdb=" O SER E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 336 through 350 Processing helix chain 'E' and resid 369 through 381 Processing helix chain 'E' and resid 388 through 403 removed outlier: 3.734A pdb=" N SER E 402 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 438 removed outlier: 3.625A pdb=" N ILE E 420 " --> pdb=" O THR E 416 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS E 421 " --> pdb=" O PHE E 417 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLN E 422 " --> pdb=" O THR E 418 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 425 " --> pdb=" O CYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 479 removed outlier: 3.784A pdb=" N ARG E 476 " --> pdb=" O GLY E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 525 through 533 Processing helix chain 'E' and resid 555 through 573 removed outlier: 3.532A pdb=" N ARG E 558 " --> pdb=" O SER E 555 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR E 559 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG E 560 " --> pdb=" O ASP E 557 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 570 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 188 through 201 removed outlier: 4.702A pdb=" N ARG F 191 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 200 " --> pdb=" O TYR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 225 removed outlier: 3.899A pdb=" N SER F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 256 through 278 removed outlier: 3.915A pdb=" N GLU F 268 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 344 Processing helix chain 'F' and resid 418 through 429 Processing helix chain 'F' and resid 461 through 473 removed outlier: 3.551A pdb=" N HIS F 465 " --> pdb=" O SER F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 546 removed outlier: 3.911A pdb=" N LYS F 537 " --> pdb=" O PRO F 533 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 541 " --> pdb=" O LYS F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 566 Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.632A pdb=" N ASN G 174 " --> pdb=" O PRO G 171 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR G 175 " --> pdb=" O TRP G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 171 through 175' Processing helix chain 'G' and resid 190 through 201 removed outlier: 3.692A pdb=" N MET G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 225 removed outlier: 3.521A pdb=" N LEU G 221 " --> pdb=" O MET G 218 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA G 224 " --> pdb=" O LEU G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 278 removed outlier: 3.693A pdb=" N ALA G 271 " --> pdb=" O GLN G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 344 Processing helix chain 'G' and resid 461 through 473 Processing helix chain 'G' and resid 533 through 546 Processing helix chain 'G' and resid 563 through 566 Processing helix chain 'H' and resid 8 through 18 Processing helix chain 'K' and resid 2 through 11 removed outlier: 3.746A pdb=" N HIS K 10 " --> pdb=" O GLN K 6 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA K 11 " --> pdb=" O GLY K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 39 Processing helix chain 'K' and resid 45 through 53 Processing helix chain 'K' and resid 55 through 58 No H-bonds generated for 'chain 'K' and resid 55 through 58' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 71 through 85 Processing helix chain 'K' and resid 88 through 91 No H-bonds generated for 'chain 'K' and resid 88 through 91' Processing helix chain 'K' and resid 100 through 120 removed outlier: 3.795A pdb=" N LYS K 104 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA K 116 " --> pdb=" O ASN K 112 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS K 117 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N THR K 118 " --> pdb=" O ARG K 114 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 137 removed outlier: 3.742A pdb=" N LYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG K 132 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 144 No H-bonds generated for 'chain 'K' and resid 142 through 144' Processing helix chain 'K' and resid 147 through 164 Processing helix chain 'K' and resid 182 through 193 removed outlier: 3.776A pdb=" N VAL K 186 " --> pdb=" O SER K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 209 through 225 removed outlier: 4.729A pdb=" N VAL K 213 " --> pdb=" O GLU K 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS K 224 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU K 225 " --> pdb=" O ILE K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 232 Processing helix chain 'K' and resid 239 through 267 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 315 through 317 No H-bonds generated for 'chain 'K' and resid 315 through 317' Processing helix chain 'K' and resid 331 through 347 Processing helix chain 'K' and resid 349 through 357 Processing helix chain 'K' and resid 367 through 386 Processing helix chain 'K' and resid 389 through 393 removed outlier: 4.048A pdb=" N GLU K 393 " --> pdb=" O HIS K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 398 No H-bonds generated for 'chain 'K' and resid 396 through 398' Processing helix chain 'K' and resid 401 through 420 Processing helix chain 'K' and resid 424 through 453 removed outlier: 3.602A pdb=" N LYS K 432 " --> pdb=" O SER K 428 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR K 435 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 472 removed outlier: 3.609A pdb=" N ALA K 466 " --> pdb=" O PHE K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 477 No H-bonds generated for 'chain 'K' and resid 474 through 477' Processing helix chain 'K' and resid 479 through 486 removed outlier: 3.748A pdb=" N LYS K 486 " --> pdb=" O PHE K 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 516 Processing helix chain 'K' and resid 837 through 845 removed outlier: 3.922A pdb=" N LYS K 843 " --> pdb=" O SER K 839 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE K 844 " --> pdb=" O TYR K 840 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER K 845 " --> pdb=" O VAL K 841 " (cutoff:3.500A) Processing helix chain 'K' and resid 847 through 859 removed outlier: 5.147A pdb=" N TRP K 852 " --> pdb=" O ASP K 848 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR K 853 " --> pdb=" O VAL K 849 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN K 858 " --> pdb=" O VAL K 854 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP K 859 " --> pdb=" O PHE K 855 " (cutoff:3.500A) Processing helix chain 'K' and resid 865 through 880 removed outlier: 3.706A pdb=" N ILE K 878 " --> pdb=" O MET K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 885 through 887 No H-bonds generated for 'chain 'K' and resid 885 through 887' Processing helix chain 'K' and resid 891 through 906 removed outlier: 4.108A pdb=" N VAL K 896 " --> pdb=" O SER K 892 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS K 906 " --> pdb=" O GLU K 902 " (cutoff:3.500A) Processing helix chain 'K' and resid 909 through 914 removed outlier: 3.714A pdb=" N LYS K 913 " --> pdb=" O LYS K 909 " (cutoff:3.500A) Processing helix chain 'K' and resid 918 through 934 removed outlier: 4.550A pdb=" N LYS K 934 " --> pdb=" O LYS K 930 " (cutoff:3.500A) Processing helix chain 'K' and resid 937 through 944 removed outlier: 4.226A pdb=" N LEU K 944 " --> pdb=" O ALA K 940 " (cutoff:3.500A) Processing helix chain 'K' and resid 949 through 956 Processing helix chain 'L' and resid 57 through 61 Processing helix chain 'L' and resid 66 through 75 removed outlier: 4.742A pdb=" N ASP L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 102 removed outlier: 3.676A pdb=" N LYS L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 120 removed outlier: 4.839A pdb=" N THR L 120 " --> pdb=" O GLU L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 131 Processing sheet with id= A, first strand: chain '2' and resid 203 through 207 removed outlier: 6.438A pdb=" N LYS 2 258 " --> pdb=" O LEU 2 204 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL 2 206 " --> pdb=" O LYS 2 258 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG 2 260 " --> pdb=" O VAL 2 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 369 through 375 removed outlier: 3.721A pdb=" N ILE 2 290 " --> pdb=" O THR 2 353 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN 2 355 " --> pdb=" O VAL 2 288 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL 2 288 " --> pdb=" O GLN 2 355 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET 2 280 " --> pdb=" O TYR 2 394 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL 2 393 " --> pdb=" O ALA 2 417 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA 2 417 " --> pdb=" O VAL 2 393 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR 2 395 " --> pdb=" O ILE 2 415 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE 2 415 " --> pdb=" O THR 2 395 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN 2 397 " --> pdb=" O THR 2 413 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N THR 2 413 " --> pdb=" O ASN 2 397 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 303 through 305 Processing sheet with id= D, first strand: chain '2' and resid 634 through 638 Processing sheet with id= E, first strand: chain '2' and resid 583 through 588 Processing sheet with id= F, first strand: chain '2' and resid 833 through 837 Processing sheet with id= G, first strand: chain '2' and resid 295 through 300 removed outlier: 6.845A pdb=" N VAL 2 345 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 52 through 56 removed outlier: 6.750A pdb=" N HIS 3 104 " --> pdb=" O LEU 3 53 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N MET 3 55 " --> pdb=" O HIS 3 104 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY 3 106 " --> pdb=" O MET 3 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain '3' and resid 221 through 227 removed outlier: 3.995A pdb=" N THR 3 205 " --> pdb=" O LYS 3 138 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS 3 138 " --> pdb=" O THR 3 205 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN 3 207 " --> pdb=" O VAL 3 136 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL 3 136 " --> pdb=" O GLN 3 207 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL 3 245 " --> pdb=" O ILE 3 267 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE 3 267 " --> pdb=" O VAL 3 245 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG 3 247 " --> pdb=" O ILE 3 265 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE 3 265 " --> pdb=" O ARG 3 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU 3 249 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER 3 263 " --> pdb=" O LEU 3 249 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 158 through 163 removed outlier: 3.734A pdb=" N LYS 3 158 " --> pdb=" O CYS 3 153 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL 3 197 " --> pdb=" O LEU 3 147 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 484 through 488 removed outlier: 6.716A pdb=" N GLY 3 407 " --> pdb=" O SER 3 450 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU 3 452 " --> pdb=" O GLY 3 407 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL 3 409 " --> pdb=" O LEU 3 452 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA 3 454 " --> pdb=" O VAL 3 409 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE 3 411 " --> pdb=" O ALA 3 454 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 383 through 386 Processing sheet with id= M, first strand: chain '3' and resid 433 through 438 Processing sheet with id= N, first strand: chain '3' and resid 604 through 606 Processing sheet with id= O, first strand: chain '4' and resid 171 through 175 removed outlier: 6.548A pdb=" N GLU 4 222 " --> pdb=" O ILE 4 172 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU 4 174 " --> pdb=" O GLU 4 222 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG 4 224 " --> pdb=" O LEU 4 174 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '4' and resid 332 through 338 removed outlier: 4.183A pdb=" N ARG 4 254 " --> pdb=" O LYS 4 316 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLN 4 318 " --> pdb=" O VAL 4 252 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL 4 252 " --> pdb=" O GLN 4 318 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE 4 356 " --> pdb=" O ALA 4 381 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA 4 381 " --> pdb=" O ILE 4 356 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG 4 358 " --> pdb=" O ILE 4 379 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE 4 379 " --> pdb=" O ARG 4 358 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR 4 360 " --> pdb=" O THR 4 377 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR 4 377 " --> pdb=" O THR 4 360 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 275 through 279 Processing sheet with id= R, first strand: chain '4' and resid 605 through 609 Processing sheet with id= S, first strand: chain '4' and resid 504 through 508 Processing sheet with id= T, first strand: chain '4' and resid 554 through 559 Processing sheet with id= U, first strand: chain '4' and resid 259 through 264 removed outlier: 7.170A pdb=" N VAL 4 308 " --> pdb=" O ARG 4 263 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '5' and resid 69 through 73 removed outlier: 6.292A pdb=" N GLN 5 125 " --> pdb=" O LEU 5 70 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE 5 72 " --> pdb=" O GLN 5 125 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR 5 127 " --> pdb=" O ILE 5 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain '5' and resid 245 through 251 removed outlier: 3.721A pdb=" N ALA 5 157 " --> pdb=" O LYS 5 229 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN 5 231 " --> pdb=" O ILE 5 155 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE 5 155 " --> pdb=" O GLN 5 231 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL 5 269 " --> pdb=" O VAL 5 295 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL 5 295 " --> pdb=" O VAL 5 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER 5 271 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU 5 293 " --> pdb=" O SER 5 271 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 170 through 172 Processing sheet with id= Y, first strand: chain '5' and resid 515 through 518 removed outlier: 6.578A pdb=" N GLY 5 439 " --> pdb=" O SER 5 482 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU 5 484 " --> pdb=" O GLY 5 439 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL 5 441 " --> pdb=" O LEU 5 484 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA 5 486 " --> pdb=" O VAL 5 441 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE 5 443 " --> pdb=" O ALA 5 486 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '5' and resid 465 through 470 removed outlier: 3.731A pdb=" N THR 5 475 " --> pdb=" O ILE 5 468 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '5' and resid 162 through 167 removed outlier: 6.711A pdb=" N GLU 5 221 " --> pdb=" O THR 5 166 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '6' and resid 54 through 58 removed outlier: 6.777A pdb=" N TYR 6 110 " --> pdb=" O ILE 6 55 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE 6 57 " --> pdb=" O TYR 6 110 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER 6 112 " --> pdb=" O ILE 6 57 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain '6' and resid 222 through 228 removed outlier: 3.729A pdb=" N ARG 6 142 " --> pdb=" O ARG 6 206 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN 6 208 " --> pdb=" O ILE 6 140 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE 6 140 " --> pdb=" O GLN 6 208 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR 6 246 " --> pdb=" O ALA 6 299 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA 6 299 " --> pdb=" O THR 6 246 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE 6 248 " --> pdb=" O PHE 6 297 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE 6 297 " --> pdb=" O ILE 6 248 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE 6 250 " --> pdb=" O MET 6 295 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N MET 6 295 " --> pdb=" O ILE 6 250 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '6' and resid 154 through 157 removed outlier: 4.550A pdb=" N CYS 6 154 " --> pdb=" O ASP 6 193 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 533 through 537 removed outlier: 3.508A pdb=" N VAL 6 393 " --> pdb=" O ILE 6 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY 6 397 " --> pdb=" O ALA 6 504 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY 6 456 " --> pdb=" O SER 6 499 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU 6 501 " --> pdb=" O GLY 6 456 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYS 6 458 " --> pdb=" O LEU 6 501 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA 6 503 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE 6 460 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE 6 418 " --> pdb=" O CYS 6 459 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP 6 461 " --> pdb=" O ILE 6 418 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR 6 420 " --> pdb=" O ASP 6 461 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '6' and resid 432 through 436 Processing sheet with id= AG, first strand: chain '6' and resid 482 through 487 Processing sheet with id= AH, first strand: chain '6' and resid 788 through 790 Processing sheet with id= AI, first strand: chain '6' and resid 147 through 152 removed outlier: 7.002A pdb=" N THR 6 198 " --> pdb=" O SER 6 151 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '7' and resid 52 through 56 removed outlier: 6.571A pdb=" N GLU 7 148 " --> pdb=" O ILE 7 53 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL 7 55 " --> pdb=" O GLU 7 148 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR 7 150 " --> pdb=" O VAL 7 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain '7' and resid 265 through 271 removed outlier: 3.603A pdb=" N ARG 7 182 " --> pdb=" O LYS 7 249 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN 7 251 " --> pdb=" O VAL 7 180 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL 7 180 " --> pdb=" O GLN 7 251 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL 7 289 " --> pdb=" O ALA 7 312 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA 7 312 " --> pdb=" O VAL 7 289 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU 7 291 " --> pdb=" O LEU 7 310 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU 7 310 " --> pdb=" O LEU 7 291 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 203 through 207 removed outlier: 4.378A pdb=" N THR 7 194 " --> pdb=" O GLN 7 236 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 373 through 375 removed outlier: 3.531A pdb=" N ASN 7 373 " --> pdb=" O ILE 7 380 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 526 through 530 Processing sheet with id= AO, first strand: chain '7' and resid 425 through 429 Processing sheet with id= AP, first strand: chain '7' and resid 475 through 480 Processing sheet with id= AQ, first strand: chain '7' and resid 187 through 192 removed outlier: 6.597A pdb=" N LYS 7 241 " --> pdb=" O GLU 7 191 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 179 through 184 removed outlier: 4.182A pdb=" N SER A 179 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'A' and resid 163 through 166 Processing sheet with id= AT, first strand: chain 'B' and resid 42 through 46 Processing sheet with id= AU, first strand: chain 'C' and resid 56 through 61 Processing sheet with id= AV, first strand: chain 'D' and resid 204 through 208 removed outlier: 4.427A pdb=" N TYR D 172 " --> pdb=" O MET D 224 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'D' and resid 182 through 186 Processing sheet with id= AX, first strand: chain 'E' and resid 51 through 55 removed outlier: 6.324A pdb=" N ILE E 96 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU E 77 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE E 98 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 270 through 276 Processing sheet with id= AZ, first strand: chain 'E' and resid 447 through 451 removed outlier: 8.094A pdb=" N PHE E 450 " --> pdb=" O PRO E 489 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE E 491 " --> pdb=" O PHE E 450 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'F' and resid 146 through 149 removed outlier: 4.545A pdb=" N THR F 592 " --> pdb=" O THR F 581 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR F 581 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL F 556 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS F 161 " --> pdb=" O MET F 561 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 509 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'F' and resid 501 through 504 removed outlier: 3.602A pdb=" N THR F 490 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 293 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS F 325 " --> pdb=" O MET F 299 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'G' and resid 146 through 149 removed outlier: 4.467A pdb=" N THR G 592 " --> pdb=" O THR G 581 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR G 581 " --> pdb=" O THR G 592 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL G 556 " --> pdb=" O ILE G 584 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER G 509 " --> pdb=" O VAL G 182 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'G' and resid 501 through 504 removed outlier: 3.609A pdb=" N PHE G 227 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 289 " --> pdb=" O CYS G 292 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN G 293 " --> pdb=" O THR G 331 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS G 325 " --> pdb=" O MET G 299 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'K' and resid 13 through 16 Processing sheet with id= BF, first strand: chain 'K' and resid 522 through 525 Processing sheet with id= BG, first strand: chain 'K' and resid 275 through 281 removed outlier: 3.772A pdb=" N GLN K 289 " --> pdb=" O ILE K 277 " (cutoff:3.500A) 2174 hydrogen bonds defined for protein. 5991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 21.33 Time building geometry restraints manager: 17.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13843 1.34 - 1.46: 11377 1.46 - 1.58: 28920 1.58 - 1.70: 150 1.70 - 1.83: 533 Bond restraints: 54823 Sorted by residual: bond pdb=" O3A ANP 6 903 " pdb=" PB ANP 6 903 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" O3A ANP 41502 " pdb=" PB ANP 41502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" O3A ANP 71500 " pdb=" PB ANP 71500 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP 31502 " pdb=" PB ANP 31502 " ideal model delta sigma weight residual 1.700 1.562 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" N3B ANP 6 903 " pdb=" PG ANP 6 903 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 54818 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.48: 1135 104.48 - 111.94: 24858 111.94 - 119.40: 21454 119.40 - 126.86: 26149 126.86 - 134.31: 729 Bond angle restraints: 74325 Sorted by residual: angle pdb=" N VAL 6 288 " pdb=" CA VAL 6 288 " pdb=" C VAL 6 288 " ideal model delta sigma weight residual 113.71 107.34 6.37 9.50e-01 1.11e+00 4.50e+01 angle pdb=" N SER 6 330 " pdb=" CA SER 6 330 " pdb=" C SER 6 330 " ideal model delta sigma weight residual 111.03 117.36 -6.33 1.11e+00 8.12e-01 3.25e+01 angle pdb=" PB ANP 6 903 " pdb=" N3B ANP 6 903 " pdb=" PG ANP 6 903 " ideal model delta sigma weight residual 126.95 110.28 16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " pdb=" CG TYR A 41 " ideal model delta sigma weight residual 113.90 122.53 -8.63 1.80e+00 3.09e-01 2.30e+01 angle pdb=" PB ANP 41502 " pdb=" N3B ANP 41502 " pdb=" PG ANP 41502 " ideal model delta sigma weight residual 126.95 113.43 13.52 3.00e+00 1.11e-01 2.03e+01 ... (remaining 74320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.69: 32044 26.69 - 53.38: 1289 53.38 - 80.06: 183 80.06 - 106.75: 31 106.75 - 133.44: 3 Dihedral angle restraints: 33550 sinusoidal: 14317 harmonic: 19233 Sorted by residual: dihedral pdb=" CA ASP 5 524 " pdb=" C ASP 5 524 " pdb=" N VAL 5 525 " pdb=" CA VAL 5 525 " ideal model delta harmonic sigma weight residual -180.00 -148.58 -31.42 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA MET 6 329 " pdb=" C MET 6 329 " pdb=" N SER 6 330 " pdb=" CA SER 6 330 " ideal model delta harmonic sigma weight residual 180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ASP F 473 " pdb=" C ASP F 473 " pdb=" N SER F 474 " pdb=" CA SER F 474 " ideal model delta harmonic sigma weight residual 180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 33547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 7538 0.082 - 0.164: 829 0.164 - 0.246: 56 0.246 - 0.329: 6 0.329 - 0.411: 4 Chirality restraints: 8433 Sorted by residual: chirality pdb=" P DG J 18 " pdb=" OP1 DG J 18 " pdb=" OP2 DG J 18 " pdb=" O5' DG J 18 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" P DA M 1 " pdb=" OP1 DA M 1 " pdb=" OP2 DA M 1 " pdb=" O5' DA M 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" P DT I 4 " pdb=" OP1 DT I 4 " pdb=" OP2 DT I 4 " pdb=" O5' DT I 4 " both_signs ideal model delta sigma weight residual True 2.35 2.73 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 8430 not shown) Planarity restraints: 9343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE 2 150 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ILE 2 150 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE 2 150 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG 2 151 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR 4 690 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO 4 691 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 4 691 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO 4 691 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 191 " 0.247 9.50e-02 1.11e+02 1.11e-01 7.55e+00 pdb=" NE ARG F 191 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG F 191 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 191 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 191 " 0.009 2.00e-02 2.50e+03 ... (remaining 9340 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 125 2.59 - 3.16: 40780 3.16 - 3.74: 77801 3.74 - 4.32: 108552 4.32 - 4.90: 182020 Nonbonded interactions: 409278 Sorted by model distance: nonbonded pdb="MG MG 31501 " pdb=" O2G ANP 31502 " model vdw 2.008 2.170 nonbonded pdb=" OG SER 3 355 " pdb="MG MG 31501 " model vdw 2.015 2.170 nonbonded pdb=" OG SER 7 397 " pdb="MG MG 71501 " model vdw 2.022 2.170 nonbonded pdb=" O2G ANP 71500 " pdb="MG MG 71501 " model vdw 2.022 2.170 nonbonded pdb="MG MG 31501 " pdb=" O2B ANP 31502 " model vdw 2.032 2.170 ... (remaining 409273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and (resid 145 through 351 or resid 455 through 594)) selection = (chain 'G' and (resid 145 through 300 or resid 324 through 594)) } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.060 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 125.650 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 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 : 0.006 0.150 54823 Z= 0.373 Angle : 0.909 16.668 74325 Z= 0.519 Chirality : 0.052 0.411 8433 Planarity : 0.007 0.111 9343 Dihedral : 14.707 133.440 21020 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.31 (0.10), residues: 6460 helix: 0.61 (0.09), residues: 2928 sheet: 0.43 (0.16), residues: 1002 loop : -0.20 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 425 HIS 0.013 0.002 HIS 4 393 PHE 0.025 0.003 PHE 2 862 TYR 0.026 0.002 TYR G 239 ARG 0.013 0.001 ARG 3 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1026 time to evaluate : 4.744 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: 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: 2 275 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8392 (pp30) REVERT: 2 779 THR cc_start: 0.7253 (p) cc_final: 0.6953 (t) REVERT: 3 264 ILE cc_start: 0.9241 (pt) cc_final: 0.8730 (pt) REVERT: 4 121 PHE cc_start: 0.6530 (t80) cc_final: 0.6266 (t80) REVERT: 4 280 VAL cc_start: 0.8813 (t) cc_final: 0.7681 (p) REVERT: 5 72 ILE cc_start: 0.9390 (mt) cc_final: 0.9118 (mm) REVERT: 5 320 MET cc_start: 0.6636 (mtm) cc_final: 0.6303 (mtp) REVERT: 5 433 MET cc_start: 0.3790 (tpt) cc_final: 0.3194 (ptt) REVERT: 6 239 ASP cc_start: 0.7116 (m-30) cc_final: 0.6775 (m-30) REVERT: 6 243 ILE cc_start: 0.8983 (mp) cc_final: 0.8456 (mm) REVERT: 7 208 VAL cc_start: 0.8847 (t) cc_final: 0.8644 (m) REVERT: 7 240 SER cc_start: 0.7890 (m) cc_final: 0.7558 (p) REVERT: A 178 ASP cc_start: 0.7891 (m-30) cc_final: 0.7597 (m-30) REVERT: B 54 LYS cc_start: 0.9353 (tptt) cc_final: 0.8952 (tppt) REVERT: B 94 GLU cc_start: 0.8861 (mp0) cc_final: 0.8497 (mp0) REVERT: B 106 ASP cc_start: 0.7781 (m-30) cc_final: 0.6994 (m-30) REVERT: C 62 TYR cc_start: 0.7893 (m-80) cc_final: 0.7638 (m-10) REVERT: D 170 MET cc_start: 0.8759 (mmm) cc_final: 0.8376 (mmm) REVERT: F 242 ILE cc_start: 0.7825 (mt) cc_final: 0.7526 (tp) REVERT: G 295 LEU cc_start: 0.6913 (tp) cc_final: 0.6687 (tt) REVERT: K 85 CYS cc_start: 0.8563 (m) cc_final: 0.7953 (m) REVERT: K 104 LYS cc_start: 0.9139 (tmtt) cc_final: 0.7986 (tttp) REVERT: L 106 MET cc_start: 0.8138 (ttp) cc_final: 0.6821 (ttm) outliers start: 22 outliers final: 2 residues processed: 1045 average time/residue: 0.5505 time to fit residues: 928.8407 Evaluate side-chains 501 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 498 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain G residue 251 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 551 optimal weight: 3.9990 chunk 494 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 511 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 380 optimal weight: 0.3980 chunk 592 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 263 GLN 2 297 GLN 2 347 HIS 2 355 GLN ** 2 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 128 ASN 3 284 GLN 3 503 HIS 4 143 HIS 4 394 GLN 4 657 ASN 5 75 ASN 5 464 GLN 5 478 ASN 5 604 ASN 6 10 GLN 6 211 GLN ** 6 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 303 GLN 6 728 HIS 6 802 HIS 7 236 GLN 7 474 GLN 7 551 GLN B 139 ASN C 101 GLN C 147 HIS F 196 GLN F 424 GLN F 469 ASN F 578 ASN G 196 GLN G 469 ASN G 528 ASN ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 469 HIS L 131 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 54823 Z= 0.247 Angle : 0.621 12.220 74325 Z= 0.330 Chirality : 0.042 0.219 8433 Planarity : 0.005 0.053 9343 Dihedral : 12.293 136.629 7986 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.77 % Allowed : 8.54 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.10), residues: 6460 helix: 1.33 (0.09), residues: 2906 sheet: 0.49 (0.15), residues: 1092 loop : 0.06 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 425 HIS 0.008 0.001 HIS K 183 PHE 0.024 0.002 PHE 5 668 TYR 0.058 0.001 TYR A 41 ARG 0.008 0.001 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 458 time to evaluate : 4.711 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: 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: 2 275 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8569 (pp30) REVERT: 2 703 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6678 (pp20) REVERT: 2 779 THR cc_start: 0.7011 (p) cc_final: 0.6535 (t) REVERT: 3 200 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8148 (p0) REVERT: 4 343 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7585 (mm-30) REVERT: 4 435 VAL cc_start: 0.8806 (t) cc_final: 0.8596 (m) REVERT: 4 677 MET cc_start: 0.7384 (mtm) cc_final: 0.7159 (mtp) REVERT: 5 609 MET cc_start: 0.6836 (mmp) cc_final: 0.6217 (mmm) REVERT: 5 650 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7178 (mtm) REVERT: 7 428 MET cc_start: 0.7367 (tmm) cc_final: 0.7080 (tmm) REVERT: A 178 ASP cc_start: 0.8147 (m-30) cc_final: 0.7887 (m-30) REVERT: A 190 MET cc_start: 0.8281 (mmm) cc_final: 0.8062 (mmm) REVERT: B 106 ASP cc_start: 0.7672 (m-30) cc_final: 0.7286 (m-30) REVERT: C 62 TYR cc_start: 0.8159 (m-80) cc_final: 0.7938 (m-10) REVERT: D 159 MET cc_start: 0.7423 (tpp) cc_final: 0.7134 (ttt) REVERT: D 170 MET cc_start: 0.8655 (mmm) cc_final: 0.8394 (mmm) REVERT: E 481 MET cc_start: 0.8248 (mmm) cc_final: 0.8023 (mmm) REVERT: F 548 MET cc_start: 0.6849 (mtt) cc_final: 0.6323 (mtt) REVERT: G 539 MET cc_start: 0.6950 (mtp) cc_final: 0.6447 (ppp) outliers start: 103 outliers final: 49 residues processed: 537 average time/residue: 0.5108 time to fit residues: 464.3270 Evaluate side-chains 426 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 373 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 2 residue 703 GLU Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 452 LEU Chi-restraints excluded: chain 3 residue 472 ILE Chi-restraints excluded: chain 3 residue 615 LEU Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 713 VAL Chi-restraints excluded: chain 5 residue 242 MET Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 5 residue 650 MET Chi-restraints excluded: chain 6 residue 28 LEU Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 440 SER Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 580 THR Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 475 ASP Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 592 THR Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain K residue 306 ASP Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 131 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 329 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 493 optimal weight: 3.9990 chunk 403 optimal weight: 5.9990 chunk 163 optimal weight: 0.3980 chunk 594 optimal weight: 0.0370 chunk 641 optimal weight: 0.7980 chunk 529 optimal weight: 0.0470 chunk 589 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 476 optimal weight: 6.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 ASN ** 2 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 464 GLN ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 267 ASN 6 623 GLN 6 783 HIS B 166 GLN ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 54823 Z= 0.139 Angle : 0.527 13.218 74325 Z= 0.278 Chirality : 0.040 0.238 8433 Planarity : 0.004 0.049 9343 Dihedral : 11.834 134.784 7982 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.40 % Allowed : 9.40 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.10), residues: 6460 helix: 1.52 (0.10), residues: 2925 sheet: 0.64 (0.15), residues: 1109 loop : 0.20 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 6 326 HIS 0.017 0.001 HIS 5 539 PHE 0.021 0.001 PHE 4 630 TYR 0.048 0.001 TYR A 41 ARG 0.006 0.000 ARG 6 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 416 time to evaluate : 4.877 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: symmetry clash REVERT: 2 680 MET cc_start: 0.5880 (mpp) cc_final: 0.5648 (mpp) REVERT: 2 779 THR cc_start: 0.6909 (p) cc_final: 0.6444 (t) REVERT: 3 45 MET cc_start: 0.7984 (ttm) cc_final: 0.7755 (ttm) REVERT: 3 175 THR cc_start: 0.6897 (t) cc_final: 0.6490 (m) REVERT: 3 200 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8070 (p0) REVERT: 4 538 MET cc_start: 0.6944 (mmm) cc_final: 0.6355 (mmm) REVERT: 5 86 MET cc_start: 0.8791 (tpp) cc_final: 0.8554 (tpp) REVERT: 6 329 MET cc_start: 0.7181 (ppp) cc_final: 0.6891 (ppp) REVERT: 6 528 MET cc_start: 0.5364 (mtt) cc_final: 0.5094 (mtt) REVERT: A 178 ASP cc_start: 0.8148 (m-30) cc_final: 0.7878 (m-30) REVERT: A 190 MET cc_start: 0.8130 (mmm) cc_final: 0.7826 (mmm) REVERT: B 106 ASP cc_start: 0.7379 (m-30) cc_final: 0.7102 (m-30) REVERT: C 62 TYR cc_start: 0.8123 (m-80) cc_final: 0.7875 (m-10) REVERT: C 171 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 159 MET cc_start: 0.7397 (tpp) cc_final: 0.7026 (ttt) REVERT: E 481 MET cc_start: 0.8106 (mmm) cc_final: 0.7872 (mmm) REVERT: F 164 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6858 (mp) REVERT: F 195 MET cc_start: 0.7379 (tmm) cc_final: 0.7152 (tmm) REVERT: F 548 MET cc_start: 0.6855 (mtt) cc_final: 0.6317 (mtt) REVERT: K 105 MET cc_start: 0.7598 (tmm) cc_final: 0.7128 (tmm) outliers start: 81 outliers final: 38 residues processed: 470 average time/residue: 0.4909 time to fit residues: 394.5537 Evaluate side-chains 396 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 356 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 531 LEU Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 410 CYS Chi-restraints excluded: chain 3 residue 452 LEU Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 5 residue 242 MET Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 507 VAL Chi-restraints excluded: chain 6 residue 572 ILE Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain K residue 306 ASP Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 395 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 586 optimal weight: 0.0470 chunk 446 optimal weight: 0.6980 chunk 308 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 283 optimal weight: 9.9990 chunk 398 optimal weight: 2.9990 chunk 596 optimal weight: 9.9990 chunk 631 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 565 optimal weight: 7.9990 chunk 170 optimal weight: 0.1980 overall best weight: 1.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 186 GLN 2 200 ASN ** 2 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 356 GLN 4 318 GLN 4 527 ASN ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 541 ASN A 17 GLN B 166 GLN C 147 HIS F 246 GLN K 10 HIS K 53 HIS ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 54823 Z= 0.197 Angle : 0.533 10.534 74325 Z= 0.281 Chirality : 0.040 0.267 8433 Planarity : 0.004 0.046 9343 Dihedral : 11.646 139.450 7979 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.84 % Allowed : 9.99 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 6460 helix: 1.69 (0.10), residues: 2926 sheet: 0.68 (0.16), residues: 1074 loop : 0.23 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 98 HIS 0.021 0.001 HIS 7 356 PHE 0.023 0.001 PHE C 104 TYR 0.044 0.001 TYR A 41 ARG 0.008 0.000 ARG 2 659 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 383 time to evaluate : 4.799 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: 2 575 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7201 (mt) REVERT: 2 680 MET cc_start: 0.6038 (mpp) cc_final: 0.5803 (mpp) REVERT: 2 779 THR cc_start: 0.7135 (p) cc_final: 0.6616 (t) REVERT: 3 200 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8164 (p0) REVERT: 5 523 HIS cc_start: 0.3931 (OUTLIER) cc_final: 0.3362 (t70) REVERT: 5 609 MET cc_start: 0.6506 (mmp) cc_final: 0.6031 (mmt) REVERT: 6 340 MET cc_start: 0.5291 (ptm) cc_final: 0.4507 (tmm) REVERT: 6 371 MET cc_start: 0.4668 (ttt) cc_final: 0.4153 (ttm) REVERT: 6 528 MET cc_start: 0.5319 (mtt) cc_final: 0.5067 (mtt) REVERT: A 178 ASP cc_start: 0.8190 (m-30) cc_final: 0.7905 (m-30) REVERT: A 190 MET cc_start: 0.8194 (mmm) cc_final: 0.7793 (tmm) REVERT: B 106 ASP cc_start: 0.7521 (m-30) cc_final: 0.7285 (m-30) REVERT: C 62 TYR cc_start: 0.8277 (m-80) cc_final: 0.8006 (m-10) REVERT: C 171 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8205 (tm-30) REVERT: D 159 MET cc_start: 0.7535 (tpp) cc_final: 0.7199 (ttt) REVERT: D 170 MET cc_start: 0.8807 (mmm) cc_final: 0.8520 (mmm) REVERT: E 481 MET cc_start: 0.8124 (mmm) cc_final: 0.7862 (mmm) REVERT: F 164 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6958 (mp) REVERT: F 195 MET cc_start: 0.7349 (tmm) cc_final: 0.7059 (tmm) REVERT: F 296 PHE cc_start: 0.6803 (m-80) cc_final: 0.6262 (m-80) REVERT: F 548 MET cc_start: 0.6635 (mtt) cc_final: 0.6199 (mtt) REVERT: G 558 MET cc_start: 0.6392 (tmm) cc_final: 0.4417 (mtm) REVERT: L 69 LEU cc_start: 0.9034 (mt) cc_final: 0.8629 (mp) outliers start: 107 outliers final: 58 residues processed: 466 average time/residue: 0.4883 time to fit residues: 394.6062 Evaluate side-chains 408 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 346 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 261 ILE Chi-restraints excluded: chain 2 residue 569 ASP Chi-restraints excluded: chain 2 residue 575 ILE Chi-restraints excluded: chain 2 residue 737 THR Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 452 LEU Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 4 residue 144 ASP Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 280 VAL Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 5 residue 242 MET Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 481 CYS Chi-restraints excluded: chain 5 residue 515 MET Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 6 residue 16 ASP Chi-restraints excluded: chain 6 residue 28 LEU Chi-restraints excluded: chain 6 residue 92 THR Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 440 SER Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 507 VAL Chi-restraints excluded: chain 7 residue 279 ASN Chi-restraints excluded: chain 7 residue 313 HIS Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain 7 residue 478 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 573 THR Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain K residue 235 SER Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 525 optimal weight: 0.9990 chunk 358 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 469 optimal weight: 8.9990 chunk 260 optimal weight: 0.9980 chunk 538 optimal weight: 10.0000 chunk 436 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 566 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 755 HIS 2 799 ASN 3 426 HIS 3 570 HIS 4 383 HIS 4 394 GLN 4 477 GLN 5 458 HIS 5 478 ASN ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 605 HIS ** 7 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 313 HIS 7 555 HIS 7 648 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN E 118 HIS E 315 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN K 86 GLN K 124 HIS ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 54823 Z= 0.379 Angle : 0.690 15.853 74325 Z= 0.359 Chirality : 0.044 0.215 8433 Planarity : 0.005 0.052 9343 Dihedral : 11.974 154.870 7979 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.27 % Allowed : 11.21 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.10), residues: 6460 helix: 1.28 (0.09), residues: 2900 sheet: 0.32 (0.16), residues: 1071 loop : -0.09 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 572 HIS 0.012 0.002 HIS 5 539 PHE 0.030 0.002 PHE B 92 TYR 0.043 0.002 TYR A 41 ARG 0.011 0.001 ARG 3 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 358 time to evaluate : 4.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 779 THR cc_start: 0.7319 (p) cc_final: 0.6836 (t) REVERT: 2 818 MET cc_start: 0.2956 (mtm) cc_final: 0.1445 (mmm) REVERT: 3 490 ASP cc_start: 0.4776 (OUTLIER) cc_final: 0.4455 (m-30) REVERT: 4 477 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8865 (tp40) REVERT: 5 86 MET cc_start: 0.8863 (tpp) cc_final: 0.8661 (tpp) REVERT: 5 462 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: 5 523 HIS cc_start: 0.3977 (OUTLIER) cc_final: 0.3499 (t70) REVERT: 5 609 MET cc_start: 0.6408 (mmp) cc_final: 0.6154 (mmm) REVERT: 6 494 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8191 (mt) REVERT: C 86 ASN cc_start: 0.8493 (t0) cc_final: 0.8208 (t0) REVERT: C 171 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8135 (tm-30) REVERT: D 170 MET cc_start: 0.8760 (mmm) cc_final: 0.8411 (mmm) REVERT: E 481 MET cc_start: 0.8331 (mmm) cc_final: 0.8125 (mmm) REVERT: F 164 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7113 (mp) REVERT: F 195 MET cc_start: 0.7518 (tmm) cc_final: 0.7283 (tmm) REVERT: F 548 MET cc_start: 0.6747 (mtt) cc_final: 0.6313 (mtt) REVERT: G 460 HIS cc_start: 0.0669 (OUTLIER) cc_final: -0.0434 (m90) outliers start: 132 outliers final: 74 residues processed: 466 average time/residue: 0.4870 time to fit residues: 391.5371 Evaluate side-chains 408 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 327 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 261 ILE Chi-restraints excluded: chain 2 residue 426 MET Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 2 residue 703 GLU Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 322 CYS Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 490 ASP Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 249 SER Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 477 GLN Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 242 MET Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 515 MET Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 602 LEU Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 6 residue 16 ASP Chi-restraints excluded: chain 6 residue 28 LEU Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 440 SER Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 573 ASP Chi-restraints excluded: chain 6 residue 591 ASP Chi-restraints excluded: chain 7 residue 45 ILE Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 279 ASN Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 460 HIS Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain G residue 592 THR Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain K residue 200 MET Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain K residue 431 LEU Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 212 optimal weight: 3.9990 chunk 568 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 370 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 631 optimal weight: 20.0000 chunk 524 optimal weight: 2.9990 chunk 292 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 331 optimal weight: 6.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 ASN 2 347 HIS 3 492 HIS 4 132 GLN 4 393 HIS 4 464 ASN ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 478 ASN ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 623 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN ** G 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 922 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54823 Z= 0.213 Angle : 0.560 16.568 74325 Z= 0.291 Chirality : 0.040 0.223 8433 Planarity : 0.004 0.044 9343 Dihedral : 11.801 152.350 7979 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.58 % Allowed : 12.44 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 6460 helix: 1.58 (0.10), residues: 2902 sheet: 0.45 (0.16), residues: 1074 loop : -0.04 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 6 326 HIS 0.011 0.001 HIS 5 539 PHE 0.016 0.001 PHE B 92 TYR 0.045 0.001 TYR A 41 ARG 0.007 0.000 ARG 3 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 338 time to evaluate : 4.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 429 ASP cc_start: 0.7140 (p0) cc_final: 0.6727 (p0) REVERT: 2 779 THR cc_start: 0.7304 (p) cc_final: 0.6802 (t) REVERT: 3 306 LEU cc_start: 0.7825 (tt) cc_final: 0.7612 (tt) REVERT: 5 523 HIS cc_start: 0.3840 (OUTLIER) cc_final: 0.3275 (t70) REVERT: 6 44 MET cc_start: 0.8250 (ttp) cc_final: 0.7901 (ttt) REVERT: 6 494 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8254 (mt) REVERT: B 166 GLN cc_start: 0.9102 (tp40) cc_final: 0.8787 (mm-40) REVERT: C 86 ASN cc_start: 0.8448 (t0) cc_final: 0.8171 (t0) REVERT: C 171 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8095 (tm-30) REVERT: D 170 MET cc_start: 0.8741 (mmm) cc_final: 0.8441 (mmm) REVERT: E 481 MET cc_start: 0.8251 (mmm) cc_final: 0.8049 (mmm) REVERT: F 195 MET cc_start: 0.7583 (tmm) cc_final: 0.7335 (tmm) REVERT: F 299 MET cc_start: 0.6080 (tmm) cc_final: 0.5790 (tmm) REVERT: F 548 MET cc_start: 0.6967 (mtt) cc_final: 0.6555 (mtt) REVERT: G 539 MET cc_start: 0.7812 (ptm) cc_final: 0.7610 (ptm) REVERT: K 105 MET cc_start: 0.7089 (tmm) cc_final: 0.6878 (tmm) outliers start: 92 outliers final: 59 residues processed: 408 average time/residue: 0.4847 time to fit residues: 345.2410 Evaluate side-chains 383 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 322 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 569 ASP Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 2 residue 703 GLU Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 392 LEU Chi-restraints excluded: chain 4 residue 393 HIS Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 6 residue 16 ASP Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 440 SER Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 573 ASP Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 279 ASN Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain 7 residue 418 SER Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 364 CYS Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 609 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 461 optimal weight: 9.9990 chunk 357 optimal weight: 8.9990 chunk 531 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 629 optimal weight: 8.9990 chunk 393 optimal weight: 0.4980 chunk 383 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 47 ASN 4 298 HIS 4 547 HIS ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 103 GLN ** 6 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 234 HIS ** 7 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 147 HIS D 74 GLN ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 534 HIS G 174 ASN ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 54823 Z= 0.411 Angle : 0.689 17.316 74325 Z= 0.358 Chirality : 0.044 0.568 8433 Planarity : 0.005 0.050 9343 Dihedral : 11.996 157.753 7979 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.31 % Allowed : 12.45 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 6460 helix: 1.16 (0.09), residues: 2903 sheet: 0.18 (0.16), residues: 1076 loop : -0.31 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 425 HIS 0.045 0.002 HIS 4 393 PHE 0.031 0.002 PHE B 92 TYR 0.043 0.002 TYR A 41 ARG 0.016 0.001 ARG 3 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 329 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 531 LEU cc_start: 0.4741 (OUTLIER) cc_final: 0.4396 (pp) REVERT: 2 680 MET cc_start: 0.5081 (mpp) cc_final: 0.4644 (mmp) REVERT: 3 200 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8541 (p0) REVERT: 3 490 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.5379 (m-30) REVERT: 5 462 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: 5 523 HIS cc_start: 0.4019 (OUTLIER) cc_final: 0.3404 (t70) REVERT: 5 609 MET cc_start: 0.6442 (mmp) cc_final: 0.5913 (mmt) REVERT: 6 410 VAL cc_start: 0.8492 (t) cc_final: 0.8268 (m) REVERT: A 190 MET cc_start: 0.7994 (mmm) cc_final: 0.7690 (tmm) REVERT: C 86 ASN cc_start: 0.8548 (t0) cc_final: 0.8313 (t0) REVERT: C 171 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 170 MET cc_start: 0.8766 (mmm) cc_final: 0.8387 (mmm) REVERT: F 195 MET cc_start: 0.7682 (tmm) cc_final: 0.7455 (tmm) REVERT: F 548 MET cc_start: 0.6804 (mtt) cc_final: 0.6416 (mtt) REVERT: G 173 MET cc_start: 0.1637 (mtt) cc_final: 0.1408 (mtm) REVERT: K 105 MET cc_start: 0.7503 (tmm) cc_final: 0.7250 (tmm) REVERT: L 92 MET cc_start: 0.8491 (mmm) cc_final: 0.8055 (mmm) outliers start: 134 outliers final: 85 residues processed: 435 average time/residue: 0.4686 time to fit residues: 361.6143 Evaluate side-chains 406 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 316 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 531 LEU Chi-restraints excluded: chain 2 residue 569 ASP Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 131 CYS Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 397 GLU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 490 ASP Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 3 residue 650 CYS Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 280 VAL Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 392 LEU Chi-restraints excluded: chain 4 residue 502 LEU Chi-restraints excluded: chain 4 residue 713 VAL Chi-restraints excluded: chain 5 residue 156 VAL Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 602 LEU Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 5 residue 650 MET Chi-restraints excluded: chain 6 residue 16 ASP Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 401 THR Chi-restraints excluded: chain 6 residue 420 THR Chi-restraints excluded: chain 6 residue 440 SER Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 572 ILE Chi-restraints excluded: chain 6 residue 573 ASP Chi-restraints excluded: chain 6 residue 591 ASP Chi-restraints excluded: chain 7 residue 45 ILE Chi-restraints excluded: chain 7 residue 181 ILE Chi-restraints excluded: chain 7 residue 279 ASN Chi-restraints excluded: chain 7 residue 313 HIS Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain 7 residue 418 SER Chi-restraints excluded: chain 7 residue 437 SER Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 364 CYS Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 530 GLU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 573 THR Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain G residue 592 THR Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain K residue 200 MET Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain K residue 484 ILE Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 389 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 375 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 400 optimal weight: 7.9990 chunk 428 optimal weight: 3.9990 chunk 311 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 494 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 ASN 4 547 HIS ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 231 GLN ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 211 GLN 6 557 HIS 6 610 ASN 7 356 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN F 146 GLN G 174 ASN ** G 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 54823 Z= 0.211 Angle : 0.573 18.698 74325 Z= 0.295 Chirality : 0.040 0.202 8433 Planarity : 0.004 0.048 9343 Dihedral : 11.828 154.012 7979 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.55 % Allowed : 13.43 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.10), residues: 6460 helix: 1.48 (0.10), residues: 2902 sheet: 0.27 (0.16), residues: 1086 loop : -0.16 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 6 326 HIS 0.009 0.001 HIS 5 539 PHE 0.015 0.001 PHE B 92 TYR 0.046 0.001 TYR A 41 ARG 0.004 0.000 ARG 6 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 336 time to evaluate : 5.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 531 LEU cc_start: 0.4547 (OUTLIER) cc_final: 0.4166 (pt) REVERT: 2 680 MET cc_start: 0.5698 (mpp) cc_final: 0.5331 (mmp) REVERT: 2 772 MET cc_start: 0.6756 (mmt) cc_final: 0.6537 (mmm) REVERT: 3 46 MET cc_start: 0.8452 (mpp) cc_final: 0.7923 (mtm) REVERT: 3 490 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.5463 (m-30) REVERT: 4 398 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.5039 (pm20) REVERT: 4 538 MET cc_start: 0.7411 (mmm) cc_final: 0.6887 (mmm) REVERT: 5 462 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7026 (mm-30) REVERT: 5 523 HIS cc_start: 0.3952 (OUTLIER) cc_final: 0.3221 (t70) REVERT: 5 609 MET cc_start: 0.6584 (mmp) cc_final: 0.6007 (mmt) REVERT: 6 466 MET cc_start: 0.8282 (tmm) cc_final: 0.8035 (tmm) REVERT: A 190 MET cc_start: 0.7895 (mmm) cc_final: 0.7546 (tmm) REVERT: B 166 GLN cc_start: 0.9166 (tp40) cc_final: 0.8902 (mm-40) REVERT: C 86 ASN cc_start: 0.8488 (t0) cc_final: 0.8251 (t0) REVERT: C 171 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8055 (tm-30) REVERT: D 170 MET cc_start: 0.8729 (mmm) cc_final: 0.8391 (mmm) REVERT: F 195 MET cc_start: 0.7675 (tmm) cc_final: 0.7438 (tmm) REVERT: F 548 MET cc_start: 0.6889 (mtt) cc_final: 0.6535 (mtt) REVERT: G 173 MET cc_start: 0.2029 (mtt) cc_final: 0.1777 (mtm) REVERT: K 105 MET cc_start: 0.7438 (tmm) cc_final: 0.7134 (tmm) REVERT: K 874 MET cc_start: 0.8537 (tpp) cc_final: 0.8218 (tpp) outliers start: 90 outliers final: 66 residues processed: 409 average time/residue: 0.4718 time to fit residues: 340.4672 Evaluate side-chains 387 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 316 time to evaluate : 4.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 531 LEU Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 3 residue 131 CYS Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 490 ASP Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 392 LEU Chi-restraints excluded: chain 4 residue 398 GLU Chi-restraints excluded: chain 4 residue 439 LEU Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 602 LEU Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 6 residue 16 ASP Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 401 THR Chi-restraints excluded: chain 6 residue 440 SER Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 572 ILE Chi-restraints excluded: chain 6 residue 573 ASP Chi-restraints excluded: chain 6 residue 591 ASP Chi-restraints excluded: chain 7 residue 181 ILE Chi-restraints excluded: chain 7 residue 279 ASN Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain 7 residue 418 SER Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 364 CYS Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain K residue 484 ILE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 572 optimal weight: 8.9990 chunk 602 optimal weight: 3.9990 chunk 550 optimal weight: 2.9990 chunk 586 optimal weight: 0.5980 chunk 353 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 460 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 529 optimal weight: 3.9990 chunk 554 optimal weight: 5.9990 chunk 584 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 ASN ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 211 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN F 340 HIS F 344 GLN ** G 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54823 Z= 0.173 Angle : 0.552 16.389 74325 Z= 0.283 Chirality : 0.040 0.215 8433 Planarity : 0.003 0.044 9343 Dihedral : 11.669 149.658 7979 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.41 % Allowed : 13.57 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 6460 helix: 1.64 (0.10), residues: 2901 sheet: 0.41 (0.16), residues: 1071 loop : -0.07 (0.13), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 6 326 HIS 0.011 0.001 HIS 3 37 PHE 0.013 0.001 PHE 6 202 TYR 0.045 0.001 TYR A 41 ARG 0.004 0.000 ARG 6 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 342 time to evaluate : 4.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 531 LEU cc_start: 0.4913 (OUTLIER) cc_final: 0.4579 (pt) REVERT: 2 680 MET cc_start: 0.5792 (mpp) cc_final: 0.5522 (mmp) REVERT: 3 46 MET cc_start: 0.8373 (mpp) cc_final: 0.7851 (mtm) REVERT: 3 490 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.5281 (m-30) REVERT: 4 139 MET cc_start: 0.5665 (ptp) cc_final: 0.5395 (ptp) REVERT: 4 398 GLU cc_start: 0.5367 (OUTLIER) cc_final: 0.4920 (pm20) REVERT: 4 538 MET cc_start: 0.7223 (mmm) cc_final: 0.6685 (mmm) REVERT: 5 462 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: 5 523 HIS cc_start: 0.3909 (OUTLIER) cc_final: 0.3177 (t70) REVERT: 5 609 MET cc_start: 0.6555 (mmp) cc_final: 0.5988 (mmt) REVERT: 6 340 MET cc_start: 0.4662 (ppp) cc_final: 0.4233 (ppp) REVERT: A 190 MET cc_start: 0.7936 (mmm) cc_final: 0.7595 (tmm) REVERT: B 166 GLN cc_start: 0.9154 (tp40) cc_final: 0.8859 (mm-40) REVERT: C 86 ASN cc_start: 0.8575 (t0) cc_final: 0.8359 (t0) REVERT: C 171 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8054 (tm-30) REVERT: D 159 MET cc_start: 0.7367 (ttt) cc_final: 0.6907 (ttt) REVERT: D 207 ILE cc_start: 0.9213 (tt) cc_final: 0.8993 (mm) REVERT: F 195 MET cc_start: 0.7650 (tmm) cc_final: 0.7415 (tmm) REVERT: F 548 MET cc_start: 0.6892 (mtt) cc_final: 0.6527 (mtt) REVERT: G 173 MET cc_start: 0.2009 (mtt) cc_final: 0.1756 (mtm) REVERT: G 558 MET cc_start: 0.6803 (tmm) cc_final: 0.4296 (mtm) REVERT: K 105 MET cc_start: 0.7369 (tmm) cc_final: 0.7123 (tmm) REVERT: K 508 MET cc_start: 0.8674 (ttp) cc_final: 0.8198 (tmm) REVERT: L 92 MET cc_start: 0.8396 (mmm) cc_final: 0.7935 (mmm) outliers start: 82 outliers final: 62 residues processed: 405 average time/residue: 0.4696 time to fit residues: 333.6808 Evaluate side-chains 393 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 326 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 531 LEU Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 131 CYS Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 490 ASP Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 392 LEU Chi-restraints excluded: chain 4 residue 398 GLU Chi-restraints excluded: chain 4 residue 434 ASP Chi-restraints excluded: chain 4 residue 439 LEU Chi-restraints excluded: chain 5 residue 156 VAL Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 567 MET Chi-restraints excluded: chain 5 residue 602 LEU Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 6 residue 16 ASP Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 401 THR Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 523 MET Chi-restraints excluded: chain 6 residue 572 ILE Chi-restraints excluded: chain 6 residue 573 ASP Chi-restraints excluded: chain 7 residue 181 ILE Chi-restraints excluded: chain 7 residue 279 ASN Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain 7 residue 418 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 CYS Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 385 optimal weight: 9.9990 chunk 620 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 431 optimal weight: 7.9990 chunk 650 optimal weight: 8.9990 chunk 598 optimal weight: 5.9990 chunk 518 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 118 GLN 4 393 HIS 4 527 ASN ** 5 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 76 GLN ** 6 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 267 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS E 444 ASN F 460 HIS ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN ** K 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 54823 Z= 0.434 Angle : 0.729 20.348 74325 Z= 0.373 Chirality : 0.044 0.224 8433 Planarity : 0.005 0.056 9343 Dihedral : 11.966 155.510 7979 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.52 % Allowed : 13.69 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.10), residues: 6460 helix: 1.13 (0.09), residues: 2895 sheet: 0.13 (0.16), residues: 1051 loop : -0.41 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 6 326 HIS 0.009 0.001 HIS 7 118 PHE 0.031 0.002 PHE B 92 TYR 0.049 0.002 TYR A 41 ARG 0.007 0.001 ARG 3 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 319 time to evaluate : 4.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 531 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4997 (pp) REVERT: 3 46 MET cc_start: 0.8186 (mpp) cc_final: 0.7759 (mtm) REVERT: 3 200 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8598 (p0) REVERT: 3 490 ASP cc_start: 0.5997 (OUTLIER) cc_final: 0.5402 (m-30) REVERT: 4 538 MET cc_start: 0.7221 (mmm) cc_final: 0.6730 (mmm) REVERT: 5 462 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: 5 523 HIS cc_start: 0.4028 (OUTLIER) cc_final: 0.3303 (t70) REVERT: 5 609 MET cc_start: 0.6224 (mmp) cc_final: 0.5584 (mmt) REVERT: 6 466 MET cc_start: 0.8299 (tmm) cc_final: 0.8070 (tmm) REVERT: C 86 ASN cc_start: 0.8601 (t0) cc_final: 0.8372 (t0) REVERT: C 171 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 195 MET cc_start: 0.7568 (tmm) cc_final: 0.7358 (tmm) REVERT: G 173 MET cc_start: 0.1978 (mtt) cc_final: 0.1704 (mtm) REVERT: G 558 MET cc_start: 0.6567 (tmm) cc_final: 0.3987 (mtm) REVERT: K 105 MET cc_start: 0.7619 (tmm) cc_final: 0.7327 (tmm) REVERT: K 508 MET cc_start: 0.8699 (ttp) cc_final: 0.8495 (ttp) REVERT: L 92 MET cc_start: 0.8546 (mmm) cc_final: 0.8089 (mmm) outliers start: 88 outliers final: 71 residues processed: 389 average time/residue: 0.4690 time to fit residues: 323.5790 Evaluate side-chains 383 residues out of total 5806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 307 time to evaluate : 4.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 531 LEU Chi-restraints excluded: chain 2 residue 643 ASP Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 131 CYS Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 490 ASP Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 3 residue 650 CYS Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 392 LEU Chi-restraints excluded: chain 4 residue 393 HIS Chi-restraints excluded: chain 4 residue 434 ASP Chi-restraints excluded: chain 4 residue 439 LEU Chi-restraints excluded: chain 4 residue 713 VAL Chi-restraints excluded: chain 5 residue 57 ASP Chi-restraints excluded: chain 5 residue 156 VAL Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 567 MET Chi-restraints excluded: chain 5 residue 602 LEU Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 5 residue 650 MET Chi-restraints excluded: chain 6 residue 16 ASP Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 401 THR Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 523 MET Chi-restraints excluded: chain 6 residue 572 ILE Chi-restraints excluded: chain 6 residue 573 ASP Chi-restraints excluded: chain 7 residue 181 ILE Chi-restraints excluded: chain 7 residue 279 ASN Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 397 SER Chi-restraints excluded: chain 7 residue 418 SER Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 364 CYS Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 248 ASN Chi-restraints excluded: chain G residue 299 MET Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 484 ILE Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7493 > 50: distance: 13 - 31: 9.263 distance: 17 - 37: 9.534 distance: 21 - 43: 14.937 distance: 24 - 31: 9.417 distance: 25 - 48: 14.271 distance: 31 - 32: 9.137 distance: 32 - 33: 10.404 distance: 32 - 35: 23.465 distance: 33 - 34: 4.506 distance: 33 - 37: 5.714 distance: 34 - 56: 11.810 distance: 35 - 36: 9.284 distance: 37 - 38: 12.049 distance: 38 - 39: 15.341 distance: 38 - 41: 15.518 distance: 39 - 40: 8.026 distance: 39 - 43: 7.044 distance: 40 - 65: 23.176 distance: 41 - 42: 9.827 distance: 43 - 44: 7.571 distance: 44 - 45: 10.862 distance: 44 - 47: 11.343 distance: 45 - 46: 7.332 distance: 45 - 48: 10.576 distance: 46 - 76: 25.042 distance: 48 - 49: 14.316 distance: 49 - 50: 32.864 distance: 49 - 52: 34.126 distance: 50 - 51: 28.069 distance: 50 - 56: 16.547 distance: 52 - 53: 17.105 distance: 52 - 54: 45.482 distance: 53 - 55: 11.821 distance: 56 - 57: 11.434 distance: 57 - 58: 6.056 distance: 57 - 60: 7.718 distance: 58 - 59: 10.922 distance: 58 - 65: 8.905 distance: 60 - 61: 10.524 distance: 61 - 62: 20.371 distance: 62 - 63: 10.639 distance: 62 - 64: 12.836 distance: 65 - 66: 19.517 distance: 66 - 67: 17.055 distance: 66 - 69: 14.800 distance: 67 - 68: 20.785 distance: 67 - 76: 24.820 distance: 69 - 70: 5.551 distance: 70 - 71: 30.744 distance: 70 - 72: 4.388 distance: 71 - 73: 14.564 distance: 73 - 75: 33.453 distance: 74 - 75: 12.385 distance: 76 - 77: 17.682 distance: 77 - 78: 18.353 distance: 77 - 80: 24.734 distance: 78 - 79: 15.872 distance: 78 - 84: 22.668 distance: 80 - 81: 17.201 distance: 81 - 82: 22.267 distance: 81 - 83: 9.492 distance: 84 - 85: 22.363 distance: 85 - 86: 14.838 distance: 85 - 88: 14.660 distance: 86 - 87: 10.969 distance: 86 - 95: 21.812 distance: 88 - 89: 14.975 distance: 89 - 90: 7.596 distance: 90 - 91: 13.826 distance: 91 - 92: 25.016 distance: 92 - 93: 8.921 distance: 92 - 94: 11.631 distance: 95 - 96: 25.868 distance: 96 - 97: 47.426 distance: 96 - 99: 18.977 distance: 97 - 98: 9.846 distance: 97 - 104: 65.086 distance: 99 - 100: 9.223 distance: 100 - 101: 13.103 distance: 101 - 102: 26.646 distance: 101 - 103: 15.442 distance: 105 - 106: 28.400 distance: 105 - 108: 12.383 distance: 106 - 107: 24.030 distance: 106 - 112: 8.942 distance: 108 - 109: 32.414 distance: 109 - 110: 13.387 distance: 109 - 111: 13.704