Starting phenix.real_space_refine (version: dev) on Sat Apr 9 05:52:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/04_2022/6rax_4786_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/04_2022/6rax_4786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/04_2022/6rax_4786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/04_2022/6rax_4786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/04_2022/6rax_4786_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/04_2022/6rax_4786_updated.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "2 ARG 177": "NH1" <-> "NH2" Residue "2 ARG 183": "NH1" <-> "NH2" Residue "2 ARG 189": "NH1" <-> "NH2" Residue "2 ARG 195": "NH1" <-> "NH2" Residue "2 ARG 201": "NH1" <-> "NH2" Residue "2 ARG 206": "NH1" <-> "NH2" Residue "2 ARG 292": "NH1" <-> "NH2" Residue "2 GLU 331": "OE1" <-> "OE2" Residue "2 ARG 369": "NH1" <-> "NH2" Residue "2 ASP 386": "OD1" <-> "OD2" Residue "2 ASP 389": "OD1" <-> "OD2" Residue "2 ASP 443": "OD1" <-> "OD2" Residue "2 ASP 445": "OD1" <-> "OD2" Residue "2 ARG 457": "NH1" <-> "NH2" Residue "2 ARG 461": "NH1" <-> "NH2" Residue "2 TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 488": "OE1" <-> "OE2" Residue "2 GLU 494": "OE1" <-> "OE2" Residue "2 TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 552": "NH1" <-> "NH2" Residue "2 GLU 557": "OE1" <-> "OE2" Residue "2 PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 587": "OE1" <-> "OE2" Residue "2 ARG 621": "NH1" <-> "NH2" Residue "2 PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 636": "OE1" <-> "OE2" Residue "2 ARG 641": "NH1" <-> "NH2" Residue "2 GLU 651": "OE1" <-> "OE2" Residue "2 ARG 698": "NH1" <-> "NH2" Residue "2 GLU 706": "OE1" <-> "OE2" Residue "2 ARG 709": "NH1" <-> "NH2" Residue "2 ASP 716": "OD1" <-> "OD2" Residue "2 ARG 760": "NH1" <-> "NH2" Residue "2 ARG 773": "NH1" <-> "NH2" Residue "3 ARG 43": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 ARG 58": "NH1" <-> "NH2" Residue "3 ARG 75": "NH1" <-> "NH2" Residue "3 ASP 85": "OD1" <-> "OD2" Residue "3 ARG 106": "NH1" <-> "NH2" Residue "3 GLU 125": "OE1" <-> "OE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 221": "OD1" <-> "OD2" Residue "3 ARG 225": "NH1" <-> "NH2" Residue "3 ARG 231": "NH1" <-> "NH2" Residue "3 ARG 239": "NH1" <-> "NH2" Residue "3 ARG 245": "NH1" <-> "NH2" Residue "3 ARG 254": "NH1" <-> "NH2" Residue "3 ASP 272": "OD1" <-> "OD2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 GLU 321": "OE1" <-> "OE2" Residue "3 ARG 329": "NH1" <-> "NH2" Residue "3 ARG 351": "NH1" <-> "NH2" Residue "3 ARG 359": "NH1" <-> "NH2" Residue "3 ARG 366": "NH1" <-> "NH2" Residue "3 ARG 414": "NH1" <-> "NH2" Residue "3 ARG 425": "NH1" <-> "NH2" Residue "3 ARG 453": "NH1" <-> "NH2" Residue "3 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 455": "OD1" <-> "OD2" Residue "3 ASP 485": "OD1" <-> "OD2" Residue "3 ASP 487": "OD1" <-> "OD2" Residue "3 ASP 489": "OD1" <-> "OD2" Residue "3 ASP 494": "OD1" <-> "OD2" Residue "3 ARG 498": "NH1" <-> "NH2" Residue "3 ARG 501": "NH1" <-> "NH2" Residue "3 TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 536": "OE1" <-> "OE2" Residue "3 TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 539": "OE1" <-> "OE2" Residue "3 ARG 550": "NH1" <-> "NH2" Residue "3 ARG 563": "NH1" <-> "NH2" Residue "3 ARG 590": "NH1" <-> "NH2" Residue "3 ARG 603": "NH1" <-> "NH2" Residue "3 ARG 610": "NH1" <-> "NH2" Residue "3 ARG 624": "NH1" <-> "NH2" Residue "3 ASP 634": "OD1" <-> "OD2" Residue "3 ASP 635": "OD1" <-> "OD2" Residue "4 ARG 174": "NH1" <-> "NH2" Residue "4 ASP 183": "OD1" <-> "OD2" Residue "4 ARG 227": "NH1" <-> "NH2" Residue "4 ARG 251": "NH1" <-> "NH2" Residue "4 ASP 283": "OD1" <-> "OD2" Residue "4 ARG 303": "NH1" <-> "NH2" Residue "4 ASP 321": "OD1" <-> "OD2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 341": "NH1" <-> "NH2" Residue "4 ARG 346": "NH1" <-> "NH2" Residue "4 GLU 359": "OE1" <-> "OE2" Residue "4 ASP 380": "OD1" <-> "OD2" Residue "4 ARG 425": "NH1" <-> "NH2" Residue "4 ASP 435": "OD1" <-> "OD2" Residue "4 GLU 446": "OE1" <-> "OE2" Residue "4 ARG 447": "NH1" <-> "NH2" Residue "4 ARG 463": "NH1" <-> "NH2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 503": "NH1" <-> "NH2" Residue "4 GLU 505": "OE1" <-> "OE2" Residue "4 ARG 538": "NH1" <-> "NH2" Residue "4 ARG 556": "NH1" <-> "NH2" Residue "4 GLU 591": "OE1" <-> "OE2" Residue "4 GLU 594": "OE1" <-> "OE2" Residue "4 GLU 623": "OE1" <-> "OE2" Residue "4 ARG 629": "NH1" <-> "NH2" Residue "4 ARG 663": "NH1" <-> "NH2" Residue "4 ARG 676": "NH1" <-> "NH2" Residue "4 GLU 678": "OE1" <-> "OE2" Residue "4 ARG 690": "NH1" <-> "NH2" Residue "4 ARG 697": "NH1" <-> "NH2" Residue "4 ARG 711": "NH1" <-> "NH2" Residue "4 TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 726": "NH1" <-> "NH2" Residue "4 ARG 734": "NH1" <-> "NH2" Residue "4 ARG 750": "NH1" <-> "NH2" Residue "4 GLU 761": "OE1" <-> "OE2" Residue "4 ARG 765": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 62": "NH1" <-> "NH2" Residue "5 GLU 68": "OE1" <-> "OE2" Residue "5 ASP 76": "OD1" <-> "OD2" Residue "5 GLU 89": "OE1" <-> "OE2" Residue "5 GLU 92": "OE1" <-> "OE2" Residue "5 GLU 95": "OE1" <-> "OE2" Residue "5 GLU 96": "OE1" <-> "OE2" Residue "5 ARG 99": "NH1" <-> "NH2" Residue "5 ARG 109": "NH1" <-> "NH2" Residue "5 GLU 111": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 ARG 199": "NH1" <-> "NH2" Residue "5 GLU 250": "OE1" <-> "OE2" Residue "5 ARG 251": "NH1" <-> "NH2" Residue "5 ARG 267": "NH1" <-> "NH2" Residue "5 ARG 274": "NH1" <-> "NH2" Residue "5 ARG 275": "NH1" <-> "NH2" Residue "5 ASP 276": "OD1" <-> "OD2" Residue "5 ARG 278": "NH1" <-> "NH2" Residue "5 ARG 291": "NH1" <-> "NH2" Residue "5 ARG 307": "NH1" <-> "NH2" Residue "5 ASP 314": "OD1" <-> "OD2" Residue "5 ARG 320": "NH1" <-> "NH2" Residue "5 ARG 321": "NH1" <-> "NH2" Residue "5 ASP 327": "OD1" <-> "OD2" Residue "5 GLU 330": "OE1" <-> "OE2" Residue "5 ARG 331": "NH1" <-> "NH2" Residue "5 ARG 344": "NH1" <-> "NH2" Residue "5 ARG 359": "NH1" <-> "NH2" Residue "5 ARG 361": "NH1" <-> "NH2" Residue "5 ARG 368": "NH1" <-> "NH2" Residue "5 ARG 422": "NH1" <-> "NH2" Residue "5 PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 VAL 432": "CG1" <-> "CG2" Residue "5 GLU 457": "OE1" <-> "OE2" Residue "5 GLU 498": "OE1" <-> "OE2" Residue "5 GLU 499": "OE1" <-> "OE2" Residue "5 GLU 552": "OE1" <-> "OE2" Residue "5 GLU 579": "OE1" <-> "OE2" Residue "5 ARG 584": "NH1" <-> "NH2" Residue "5 ARG 589": "NH1" <-> "NH2" Residue "5 ASP 600": "OD1" <-> "OD2" Residue "5 ARG 602": "NH1" <-> "NH2" Residue "5 GLU 620": "OE1" <-> "OE2" Residue "5 ARG 626": "NH1" <-> "NH2" Residue "5 ASP 649": "OD1" <-> "OD2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "6 ARG 95": "NH1" <-> "NH2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 ARG 118": "NH1" <-> "NH2" Residue "6 ASP 119": "OD1" <-> "OD2" Residue "6 ARG 130": "NH1" <-> "NH2" Residue "6 GLU 158": "OE1" <-> "OE2" Residue "6 ARG 160": "NH1" <-> "NH2" Residue "6 ARG 175": "NH1" <-> "NH2" Residue "6 ARG 182": "NH1" <-> "NH2" Residue "6 ARG 184": "NH1" <-> "NH2" Residue "6 GLU 190": "OE1" <-> "OE2" Residue "6 ASP 196": "OD1" <-> "OD2" Residue "6 ARG 201": "NH1" <-> "NH2" Residue "6 ARG 211": "NH1" <-> "NH2" Residue "6 ARG 216": "NH1" <-> "NH2" Residue "6 ARG 223": "NH1" <-> "NH2" Residue "6 ARG 257": "NH1" <-> "NH2" Residue "6 ARG 263": "NH1" <-> "NH2" Residue "6 ARG 282": "NH1" <-> "NH2" Residue "6 ARG 287": "NH1" <-> "NH2" Residue "6 ARG 301": "NH1" <-> "NH2" Residue "6 GLU 311": "OE1" <-> "OE2" Residue "6 ASP 316": "OD1" <-> "OD2" Residue "6 ARG 336": "NH1" <-> "NH2" Residue "6 ARG 358": "NH1" <-> "NH2" Residue "6 GLU 374": "OE1" <-> "OE2" Residue "6 ARG 379": "NH1" <-> "NH2" Residue "6 ARG 407": "NH1" <-> "NH2" Residue "6 ASP 428": "OD1" <-> "OD2" Residue "6 GLU 430": "OE1" <-> "OE2" Residue "6 GLU 453": "OE1" <-> "OE2" Residue "6 ASP 458": "OD1" <-> "OD2" Residue "6 ARG 460": "NH1" <-> "NH2" Residue "6 ARG 478": "NH1" <-> "NH2" Residue "6 ARG 482": "NH1" <-> "NH2" Residue "6 ARG 504": "NH1" <-> "NH2" Residue "6 ASP 530": "OD1" <-> "OD2" Residue "6 GLU 531": "OE1" <-> "OE2" Residue "6 ARG 542": "NH1" <-> "NH2" Residue "6 GLU 552": "OE1" <-> "OE2" Residue "6 GLU 556": "OE1" <-> "OE2" Residue "6 ARG 557": "NH1" <-> "NH2" Residue "6 ARG 561": "NH1" <-> "NH2" Residue "6 GLU 581": "OE1" <-> "OE2" Residue "6 ARG 594": "NH1" <-> "NH2" Residue "6 ARG 596": "NH1" <-> "NH2" Residue "6 ARG 603": "NH1" <-> "NH2" Residue "6 ARG 631": "NH1" <-> "NH2" Residue "6 ARG 635": "NH1" <-> "NH2" Residue "6 ARG 642": "NH1" <-> "NH2" Residue "7 ARG 3": "NH1" <-> "NH2" Residue "7 ARG 4": "NH1" <-> "NH2" Residue "7 ARG 10": "NH1" <-> "NH2" Residue "7 GLU 19": "OE1" <-> "OE2" Residue "7 GLU 30": "OE1" <-> "OE2" Residue "7 ARG 71": "NH1" <-> "NH2" Residue "7 ARG 72": "NH1" <-> "NH2" Residue "7 ASP 121": "OD1" <-> "OD2" Residue "7 ARG 123": "NH1" <-> "NH2" Residue "7 ARG 133": "NH1" <-> "NH2" Residue "7 GLU 151": "OE1" <-> "OE2" Residue "7 ARG 186": "NH1" <-> "NH2" Residue "7 ASP 209": "OD1" <-> "OD2" Residue "7 ARG 212": "NH1" <-> "NH2" Residue "7 ARG 219": "NH1" <-> "NH2" Residue "7 GLU 234": "OE1" <-> "OE2" Residue "7 ARG 258": "NH1" <-> "NH2" Residue "7 GLU 260": "OE1" <-> "OE2" Residue "7 PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 302": "NH1" <-> "NH2" Residue "7 GLU 322": "OE1" <-> "OE2" Residue "7 GLU 323": "OE1" <-> "OE2" Residue "7 GLU 325": "OE1" <-> "OE2" Residue "7 ASP 349": "OD1" <-> "OD2" Residue "7 ARG 365": "NH1" <-> "NH2" Residue "7 ASP 367": "OD1" <-> "OD2" Residue "7 ARG 372": "NH1" <-> "NH2" Residue "7 ARG 396": "NH1" <-> "NH2" Residue "7 ARG 407": "NH1" <-> "NH2" Residue "7 GLU 426": "OE1" <-> "OE2" Residue "7 ASP 448": "OD1" <-> "OD2" Residue "7 ARG 494": "NH1" <-> "NH2" Residue "7 ARG 498": "NH1" <-> "NH2" Residue "7 ARG 499": "NH1" <-> "NH2" Residue "7 PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 523": "OD1" <-> "OD2" Residue "7 ASP 526": "OD1" <-> "OD2" Residue "7 ARG 527": "NH1" <-> "NH2" Residue "7 ASP 530": "OD1" <-> "OD2" Residue "7 ARG 532": "NH1" <-> "NH2" Residue "7 ARG 550": "NH1" <-> "NH2" Residue "7 ARG 561": "NH1" <-> "NH2" Residue "7 ARG 568": "NH1" <-> "NH2" Residue "7 ASP 579": "OD1" <-> "OD2" Residue "7 ARG 590": "NH1" <-> "NH2" Residue "7 ARG 593": "NH1" <-> "NH2" Residue "7 ASP 597": "OD1" <-> "OD2" Residue "7 ARG 611": "NH1" <-> "NH2" Residue "7 ARG 618": "NH1" <-> "NH2" Residue "7 ARG 620": "NH1" <-> "NH2" Residue "7 ASP 623": "OD1" <-> "OD2" Residue "7 ARG 635": "NH1" <-> "NH2" Residue "7 ASP 642": "OD1" <-> "OD2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H ASP 162": "OD1" <-> "OD2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H ASP 170": "OD1" <-> "OD2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L ASP 106": "OD1" <-> "OD2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M ASP 45": "OD1" <-> "OD2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "M ASP 134": "OD1" <-> "OD2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "N GLU 25": "OE1" <-> "OE2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "N TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "N PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 40970 Number of models: 1 Model: "" Number of chains: 19 Chain: "2" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4788 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 28, 'TRANS': 576} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "3" Number of atoms: 4879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4879 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 22, 'TRANS': 602} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "4" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5013 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 26, 'TRANS': 599} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4864 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 592} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 4986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4986 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 608} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "7" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4964 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 4, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 24, 'TRANS': 611} Unresolved chain links: 5 Chain breaks: 2 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 19 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 424 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4575 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 14, 'TRANS': 552} Chain: "H" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1583 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1498 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1381 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1677 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ILE%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.72, per 1000 atoms: 0.51 Number of scatterers: 40970 At special positions: 0 Unit cell: (214.92, 182.52, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 239 16.00 P 44 15.00 O 7875 8.00 N 7193 7.00 C 25619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.06 Simple disulfide: pdb=" SG CYS 6 152 " - pdb=" SG CYS 6 179 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 187 " - pdb=" SG CYS 7 211 " distance=2.03 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 Atom "HETATM40909 O3A ATP 5 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.59 Conformation dependent library (CDL) restraints added in 6.1 seconds 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9610 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 29 sheets defined 31.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain '2' and resid 179 through 188 Processing helix chain '2' and resid 199 through 210 removed outlier: 4.757A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 225 Processing helix chain '2' and resid 231 through 234 No H-bonds generated for 'chain '2' and resid 231 through 234' Processing helix chain '2' and resid 237 through 255 removed outlier: 3.947A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 257 through 259 No H-bonds generated for 'chain '2' and resid 257 through 259' Processing helix chain '2' and resid 284 through 286 No H-bonds generated for 'chain '2' and resid 284 through 286' Processing helix chain '2' and resid 456 through 461 removed outlier: 3.652A pdb=" N VAL 2 459 " --> pdb=" O PRO 2 456 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG 2 461 " --> pdb=" O ILE 2 458 " (cutoff:3.500A) Processing helix chain '2' and resid 463 through 465 No H-bonds generated for 'chain '2' and resid 463 through 465' Processing helix chain '2' and resid 474 through 485 removed outlier: 4.396A pdb=" N PHE 2 485 " --> pdb=" O ALA 2 481 " (cutoff:3.500A) Processing helix chain '2' and resid 517 through 524 removed outlier: 4.405A pdb=" N THR 2 521 " --> pdb=" O PHE 2 517 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU 2 522 " --> pdb=" O LEU 2 518 " (cutoff:3.500A) Processing helix chain '2' and resid 551 through 553 No H-bonds generated for 'chain '2' and resid 551 through 553' Processing helix chain '2' and resid 579 through 582 No H-bonds generated for 'chain '2' and resid 579 through 582' Processing helix chain '2' and resid 636 through 638 No H-bonds generated for 'chain '2' and resid 636 through 638' Processing helix chain '2' and resid 654 through 667 Processing helix chain '2' and resid 694 through 706 removed outlier: 4.517A pdb=" N ARG 2 698 " --> pdb=" O GLN 2 694 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN 2 699 " --> pdb=" O ASP 2 695 " (cutoff:3.500A) Processing helix chain '2' and resid 719 through 730 Processing helix chain '2' and resid 743 through 757 removed outlier: 3.728A pdb=" N ILE 2 748 " --> pdb=" O ILE 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 765 through 781 removed outlier: 3.514A pdb=" N ILE 2 780 " --> pdb=" O LEU 2 776 " (cutoff:3.500A) Processing helix chain '2' and resid 789 through 794 Processing helix chain '3' and resid 7 through 19 removed outlier: 3.514A pdb=" N ASP 3 18 " --> pdb=" O GLU 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 59 Proline residue: 3 56 - end of helix Processing helix chain '3' and resid 69 through 84 Processing helix chain '3' and resid 86 through 88 No H-bonds generated for 'chain '3' and resid 86 through 88' Processing helix chain '3' and resid 110 through 112 No H-bonds generated for 'chain '3' and resid 110 through 112' Processing helix chain '3' and resid 202 through 204 No H-bonds generated for 'chain '3' and resid 202 through 204' Processing helix chain '3' and resid 220 through 222 No H-bonds generated for 'chain '3' and resid 220 through 222' Processing helix chain '3' and resid 277 through 286 removed outlier: 4.189A pdb=" N LYS 3 286 " --> pdb=" O LYS 3 282 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 298 removed outlier: 4.062A pdb=" N LEU 3 298 " --> pdb=" O LEU 3 294 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 316 removed outlier: 4.792A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU 3 315 " --> pdb=" O ALA 3 311 " (cutoff:3.500A) Processing helix chain '3' and resid 346 through 348 No H-bonds generated for 'chain '3' and resid 346 through 348' Processing helix chain '3' and resid 394 through 396 No H-bonds generated for 'chain '3' and resid 394 through 396' Processing helix chain '3' and resid 413 through 423 removed outlier: 4.404A pdb=" N VAL 3 420 " --> pdb=" O ALA 3 416 " (cutoff:3.500A) Processing helix chain '3' and resid 470 through 473 No H-bonds generated for 'chain '3' and resid 470 through 473' Processing helix chain '3' and resid 488 through 501 Processing helix chain '3' and resid 560 through 565 Processing helix chain '3' and resid 567 through 571 Processing helix chain '3' and resid 580 through 594 Processing helix chain '3' and resid 611 through 625 Processing helix chain '3' and resid 633 through 645 removed outlier: 4.225A pdb=" N LEU 3 642 " --> pdb=" O ALA 3 638 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL 3 643 " --> pdb=" O ALA 3 639 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 173 Processing helix chain '4' and resid 178 through 181 No H-bonds generated for 'chain '4' and resid 178 through 181' Processing helix chain '4' and resid 195 through 204 Processing helix chain '4' and resid 217 through 219 No H-bonds generated for 'chain '4' and resid 217 through 219' Processing helix chain '4' and resid 224 through 230 Processing helix chain '4' and resid 233 through 251 Proline residue: 4 238 - end of helix removed outlier: 3.647A pdb=" N ASP 4 241 " --> pdb=" O ILE 4 237 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 379 through 381 No H-bonds generated for 'chain '4' and resid 379 through 381' Processing helix chain '4' and resid 439 through 441 No H-bonds generated for 'chain '4' and resid 439 through 441' Processing helix chain '4' and resid 445 through 455 removed outlier: 3.617A pdb=" N LEU 4 450 " --> pdb=" O GLU 4 446 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 466 removed outlier: 3.526A pdb=" N TYR 4 461 " --> pdb=" O PRO 4 458 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU 4 464 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA 4 465 " --> pdb=" O ASP 4 462 " (cutoff:3.500A) Processing helix chain '4' and resid 476 through 486 removed outlier: 4.355A pdb=" N LYS 4 480 " --> pdb=" O ASP 4 477 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU 4 484 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) Processing helix chain '4' and resid 518 through 527 removed outlier: 3.641A pdb=" N ASN 4 527 " --> pdb=" O GLN 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 565 through 567 No H-bonds generated for 'chain '4' and resid 565 through 567' Processing helix chain '4' and resid 589 through 595 Processing helix chain '4' and resid 642 through 645 No H-bonds generated for 'chain '4' and resid 642 through 645' Processing helix chain '4' and resid 659 through 674 removed outlier: 3.581A pdb=" N LYS 4 662 " --> pdb=" O ILE 4 659 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER 4 666 " --> pdb=" O ARG 4 663 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU 4 668 " --> pdb=" O ALA 4 665 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU 4 671 " --> pdb=" O LEU 4 668 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 4 674 " --> pdb=" O LEU 4 671 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 697 removed outlier: 4.210A pdb=" N TYR 4 692 " --> pdb=" O VAL 4 688 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA 4 696 " --> pdb=" O TYR 4 692 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG 4 697 " --> pdb=" O ILE 4 693 " (cutoff:3.500A) Processing helix chain '4' and resid 710 through 720 removed outlier: 6.787A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) Processing helix chain '4' and resid 735 through 751 removed outlier: 4.626A pdb=" N ARG 4 750 " --> pdb=" O HIS 4 746 " (cutoff:3.500A) Processing helix chain '4' and resid 758 through 768 Processing helix chain '5' and resid 28 through 40 removed outlier: 3.854A pdb=" N LYS 5 32 " --> pdb=" O GLN 5 28 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS 5 35 " --> pdb=" O LYS 5 31 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE 5 38 " --> pdb=" O TYR 5 34 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG 5 39 " --> pdb=" O LYS 5 35 " (cutoff:3.500A) Processing helix chain '5' and resid 51 through 60 removed outlier: 4.001A pdb=" N ASN 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 75 No H-bonds generated for 'chain '5' and resid 72 through 75' Processing helix chain '5' and resid 79 through 83 Processing helix chain '5' and resid 87 through 106 removed outlier: 4.229A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU 5 95 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE 5 105 " --> pdb=" O VAL 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 132 through 134 No H-bonds generated for 'chain '5' and resid 132 through 134' Processing helix chain '5' and resid 313 through 324 Processing helix chain '5' and resid 329 through 334 removed outlier: 3.848A pdb=" N GLN 5 334 " --> pdb=" O GLU 5 330 " (cutoff:3.500A) Processing helix chain '5' and resid 352 through 355 No H-bonds generated for 'chain '5' and resid 352 through 355' Processing helix chain '5' and resid 384 through 393 Processing helix chain '5' and resid 453 through 461 removed outlier: 3.862A pdb=" N MET 5 459 " --> pdb=" O ILE 5 455 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU 5 460 " --> pdb=" O HIS 5 456 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN 5 461 " --> pdb=" O GLU 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 495 removed outlier: 3.810A pdb=" N ASP 5 494 " --> pdb=" O GLY 5 490 " (cutoff:3.500A) Processing helix chain '5' and resid 523 through 536 Processing helix chain '5' and resid 544 through 547 No H-bonds generated for 'chain '5' and resid 544 through 547' Processing helix chain '5' and resid 555 through 567 removed outlier: 4.049A pdb=" N THR 5 567 " --> pdb=" O HIS 5 563 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 598 removed outlier: 3.910A pdb=" N GLU 5 579 " --> pdb=" O GLU 5 575 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS 5 580 " --> pdb=" O ALA 5 576 " (cutoff:3.500A) Processing helix chain '5' and resid 609 through 626 removed outlier: 4.229A pdb=" N ARG 5 617 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 649 removed outlier: 4.315A pdb=" N GLU 5 638 " --> pdb=" O GLU 5 634 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA 5 639 " --> pdb=" O HIS 5 635 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) Processing helix chain '6' and resid 16 through 30 Processing helix chain '6' and resid 42 through 50 removed outlier: 4.325A pdb=" N SER 6 49 " --> pdb=" O ALA 6 45 " (cutoff:3.500A) Proline residue: 6 50 - end of helix Processing helix chain '6' and resid 59 through 65 removed outlier: 3.869A pdb=" N GLU 6 63 " --> pdb=" O PHE 6 59 " (cutoff:3.500A) Processing helix chain '6' and resid 70 through 73 No H-bonds generated for 'chain '6' and resid 70 through 73' Processing helix chain '6' and resid 77 through 93 Proline residue: 6 82 - end of helix removed outlier: 3.701A pdb=" N CYS 6 85 " --> pdb=" O TYR 6 81 " (cutoff:3.500A) Processing helix chain '6' and resid 326 through 329 No H-bonds generated for 'chain '6' and resid 326 through 329' Processing helix chain '6' and resid 331 through 333 No H-bonds generated for 'chain '6' and resid 331 through 333' Processing helix chain '6' and resid 338 through 343 Processing helix chain '6' and resid 356 through 364 removed outlier: 5.381A pdb=" N LEU 6 361 " --> pdb=" O LYS 6 357 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU 6 362 " --> pdb=" O ARG 6 358 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN 6 363 " --> pdb=" O GLY 6 359 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN 6 364 " --> pdb=" O ILE 6 360 " (cutoff:3.500A) Processing helix chain '6' and resid 396 through 399 No H-bonds generated for 'chain '6' and resid 396 through 399' Processing helix chain '6' and resid 401 through 404 No H-bonds generated for 'chain '6' and resid 401 through 404' Processing helix chain '6' and resid 461 through 468 removed outlier: 4.037A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 508 through 511 No H-bonds generated for 'chain '6' and resid 508 through 511' Processing helix chain '6' and resid 517 through 521 Processing helix chain '6' and resid 534 through 546 removed outlier: 4.166A pdb=" N ASP 6 546 " --> pdb=" O ARG 6 542 " (cutoff:3.500A) Processing helix chain '6' and resid 561 through 571 Processing helix chain '6' and resid 581 through 598 removed outlier: 4.872A pdb=" N VAL 6 587 " --> pdb=" O GLY 6 583 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU 6 588 " --> pdb=" O HIS 6 584 " (cutoff:3.500A) Processing helix chain '6' and resid 611 through 627 removed outlier: 4.424A pdb=" N GLU 6 627 " --> pdb=" O MET 6 623 " (cutoff:3.500A) Processing helix chain '6' and resid 634 through 650 Processing helix chain '7' and resid 8 through 18 Processing helix chain '7' and resid 32 through 41 Processing helix chain '7' and resid 52 through 58 Processing helix chain '7' and resid 66 through 69 No H-bonds generated for 'chain '7' and resid 66 through 69' Processing helix chain '7' and resid 72 through 83 removed outlier: 3.919A pdb=" N GLU 7 83 " --> pdb=" O ASP 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 98 through 107 Processing helix chain '7' and resid 149 through 151 No H-bonds generated for 'chain '7' and resid 149 through 151' Processing helix chain '7' and resid 224 through 226 No H-bonds generated for 'chain '7' and resid 224 through 226' Processing helix chain '7' and resid 320 through 327 removed outlier: 4.196A pdb=" N GLU 7 325 " --> pdb=" O PRO 7 321 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU 7 326 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 334 through 338 Processing helix chain '7' and resid 350 through 359 removed outlier: 3.993A pdb=" N LEU 7 357 " --> pdb=" O ALA 7 353 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 7 358 " --> pdb=" O LEU 7 354 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL 7 359 " --> pdb=" O LEU 7 355 " (cutoff:3.500A) Processing helix chain '7' and resid 366 through 368 No H-bonds generated for 'chain '7' and resid 366 through 368' Processing helix chain '7' and resid 387 through 397 removed outlier: 3.578A pdb=" N ARG 7 396 " --> pdb=" O GLY 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 411 through 413 No H-bonds generated for 'chain '7' and resid 411 through 413' Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 447 through 449 No H-bonds generated for 'chain '7' and resid 447 through 449' Processing helix chain '7' and resid 453 through 462 removed outlier: 3.896A pdb=" N GLU 7 460 " --> pdb=" O ALA 7 457 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL 7 461 " --> pdb=" O ILE 7 458 " (cutoff:3.500A) Processing helix chain '7' and resid 509 through 514 Processing helix chain '7' and resid 529 through 542 removed outlier: 3.896A pdb=" N LYS 7 535 " --> pdb=" O LEU 7 531 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS 7 536 " --> pdb=" O ARG 7 532 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR 7 539 " --> pdb=" O LYS 7 535 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER 7 542 " --> pdb=" O THR 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 556 through 567 removed outlier: 3.635A pdb=" N LEU 7 565 " --> pdb=" O ARG 7 561 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 590 removed outlier: 4.833A pdb=" N ASP 7 579 " --> pdb=" O GLU 7 576 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE 7 581 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL 7 582 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU 7 588 " --> pdb=" O TYR 7 585 " (cutoff:3.500A) Processing helix chain '7' and resid 603 through 620 removed outlier: 4.314A pdb=" N ILE 7 609 " --> pdb=" O LEU 7 606 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU 7 610 " --> pdb=" O LEU 7 607 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER 7 613 " --> pdb=" O LEU 7 610 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR 7 614 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 7 616 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG 7 620 " --> pdb=" O ALA 7 617 " (cutoff:3.500A) Processing helix chain '7' and resid 627 through 640 removed outlier: 3.812A pdb=" N ARG 7 635 " --> pdb=" O ALA 7 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 27 through 40 removed outlier: 4.103A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 Processing helix chain 'A' and resid 83 through 86 No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 184 through 200 removed outlier: 4.786A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 230 through 243 removed outlier: 4.533A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 4.361A pdb=" N LEU A 258 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 262 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 348 through 360 removed outlier: 5.726A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.288A pdb=" N ALA A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 423 through 448 removed outlier: 3.848A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 5.184A pdb=" N ARG A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 541 removed outlier: 3.559A pdb=" N GLN A 537 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.683A pdb=" N LEU H 16 " --> pdb=" O PHE H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 38 No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing helix chain 'H' and resid 40 through 48 removed outlier: 3.851A pdb=" N PHE H 45 " --> pdb=" O ILE H 41 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 97 Proline residue: H 65 - end of helix removed outlier: 3.520A pdb=" N LYS H 78 " --> pdb=" O GLN H 75 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG H 79 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU H 87 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE H 92 " --> pdb=" O CYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 132 removed outlier: 3.667A pdb=" N PHE H 119 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN H 120 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU H 126 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 7 through 10 No H-bonds generated for 'chain 'L' and resid 7 through 10' Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 70 through 80 removed outlier: 5.156A pdb=" N LYS L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 100 removed outlier: 3.980A pdb=" N GLN L 97 " --> pdb=" O MET L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 105 No H-bonds generated for 'chain 'L' and resid 103 through 105' Processing helix chain 'L' and resid 112 through 130 removed outlier: 3.892A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 150 through 155 removed outlier: 3.577A pdb=" N HIS L 154 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 150 through 155' Processing helix chain 'L' and resid 157 through 172 Proline residue: L 161 - end of helix removed outlier: 5.306A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR L 170 " --> pdb=" O HIS L 166 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLN L 171 " --> pdb=" O ILE L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 176 No H-bonds generated for 'chain 'L' and resid 174 through 176' Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 79 through 87 Processing helix chain 'M' and resid 105 through 111 Proline residue: M 110 - end of helix Processing helix chain 'M' and resid 117 through 133 removed outlier: 3.889A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU M 133 " --> pdb=" O VAL M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 171 removed outlier: 3.844A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 50 removed outlier: 4.435A pdb=" N ILE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA N 45 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET N 50 " --> pdb=" O TRP N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 80 removed outlier: 4.043A pdb=" N VAL N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU N 80 " --> pdb=" O GLN N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 114 Processing helix chain 'N' and resid 119 through 126 Processing helix chain 'N' and resid 135 through 154 removed outlier: 4.755A pdb=" N LYS N 154 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 216 No H-bonds generated for 'chain 'N' and resid 214 through 216' Processing helix chain 'N' and resid 219 through 222 No H-bonds generated for 'chain 'N' and resid 219 through 222' Processing sheet with id= A, first strand: chain '2' and resid 296 through 298 removed outlier: 4.474A pdb=" N THR 2 362 " --> pdb=" O THR 2 298 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN 2 359 " --> pdb=" O LEU 2 383 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 2 379 " --> pdb=" O LEU 2 363 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 304 through 307 Processing sheet with id= C, first strand: chain '2' and resid 310 through 312 removed outlier: 4.077A pdb=" N ILE 2 310 " --> pdb=" O PHE 2 324 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR 2 312 " --> pdb=" O GLY 2 322 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY 2 322 " --> pdb=" O TYR 2 312 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 397 through 399 Processing sheet with id= E, first strand: chain '3' and resid 197 through 199 removed outlier: 3.655A pdb=" N THR 3 197 " --> pdb=" O THR 3 129 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR 3 129 " --> pdb=" O THR 3 197 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN 3 199 " --> pdb=" O ILE 3 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL 3 235 " --> pdb=" O ASN 3 261 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN 3 261 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 135 through 138 removed outlier: 4.069A pdb=" N ARG 3 135 " --> pdb=" O HIS 3 193 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS 3 137 " --> pdb=" O LYS 3 191 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS 3 191 " --> pdb=" O LYS 3 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 140 through 142 Processing sheet with id= H, first strand: chain '3' and resid 194 through 196 removed outlier: 4.130A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 237 through 239 Processing sheet with id= J, first strand: chain '3' and resid 360 through 363 removed outlier: 7.690A pdb=" N VAL 3 400 " --> pdb=" O ILE 3 361 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N THR 3 363 " --> pdb=" O VAL 3 400 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS 3 402 " --> pdb=" O THR 3 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '4' and resid 317 through 319 removed outlier: 4.065A pdb=" N VAL 4 318 " --> pdb=" O ALA 4 305 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 4 305 " --> pdb=" O VAL 4 318 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG 4 341 " --> pdb=" O SER 4 308 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 355 through 357 Processing sheet with id= M, first strand: chain '4' and resid 391 through 394 removed outlier: 3.563A pdb=" N THR 4 392 " --> pdb=" O ARG 4 425 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS 4 423 " --> pdb=" O THR 4 394 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 397 through 400 Processing sheet with id= O, first strand: chain '4' and resid 532 through 534 removed outlier: 6.635A pdb=" N VAL 4 572 " --> pdb=" O GLN 4 533 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '4' and resid 550 through 552 removed outlier: 4.174A pdb=" N THR 4 550 " --> pdb=" O VAL 4 559 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 4 559 " --> pdb=" O THR 4 550 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '5' and resid 223 through 225 Processing sheet with id= R, first strand: chain '5' and resid 262 through 265 Processing sheet with id= S, first strand: chain '5' and resid 481 through 483 removed outlier: 6.099A pdb=" N MET 5 513 " --> pdb=" O LEU 5 375 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU 5 377 " --> pdb=" O MET 5 513 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE 5 515 " --> pdb=" O LEU 5 377 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '6' and resid 142 through 144 removed outlier: 4.294A pdb=" N PHE 6 197 " --> pdb=" O HIS 6 142 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '6' and resid 198 through 202 removed outlier: 3.846A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '7' and resid 252 through 254 removed outlier: 6.478A pdb=" N VAL 7 276 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA 7 300 " --> pdb=" O VAL 7 276 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU 7 278 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU 7 298 " --> pdb=" O LEU 7 278 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '7' and resid 175 through 177 Processing sheet with id= X, first strand: chain '7' and resid 181 through 183 removed outlier: 4.470A pdb=" N THR 7 181 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '7' and resid 364 through 366 removed outlier: 3.925A pdb=" N LYS 7 364 " --> pdb=" O ILE 7 371 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '7' and resid 401 through 404 removed outlier: 7.034A pdb=" N VAL 7 441 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N THR 7 404 " --> pdb=" O VAL 7 441 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS 7 443 " --> pdb=" O THR 7 404 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS 7 442 " --> pdb=" O SER 7 483 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU 7 485 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 18 through 20 removed outlier: 7.111A pdb=" N TYR A 71 " --> pdb=" O ILE A 19 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'A' and resid 501 through 505 removed outlier: 3.707A pdb=" N ALA A 503 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 14 through 18 896 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.11 Time building geometry restraints manager: 19.76 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: 13140 1.34 - 1.46: 9190 1.46 - 1.59: 18943 1.59 - 1.71: 83 1.71 - 1.84: 377 Bond restraints: 41733 Sorted by residual: bond pdb=" C4 ATP 3 901 " pdb=" C5 ATP 3 901 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C4 ATP 5 801 " pdb=" C5 ATP 5 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.60e+01 bond pdb=" C4 ATP 2 901 " pdb=" C5 ATP 2 901 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C5 ATP 5 801 " pdb=" C6 ATP 5 801 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.11e+01 bond pdb=" C5 ATP 2 901 " pdb=" C6 ATP 2 901 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.42e+01 ... (remaining 41728 not shown) Histogram of bond angle deviations from ideal: 94.50 - 105.46: 1009 105.46 - 116.41: 27623 116.41 - 127.37: 27445 127.37 - 138.32: 420 138.32 - 149.28: 5 Bond angle restraints: 56502 Sorted by residual: angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 117.79 22.08 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP 5 801 " pdb=" O3B ATP 5 801 " pdb=" PG ATP 5 801 " ideal model delta sigma weight residual 139.87 118.58 21.29 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PA ATP 2 901 " pdb=" O3A ATP 2 901 " pdb=" PB ATP 2 901 " ideal model delta sigma weight residual 136.83 117.36 19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP 5 801 " pdb=" O3A ATP 5 801 " pdb=" PB ATP 5 801 " ideal model delta sigma weight residual 136.83 117.38 19.45 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP 3 901 " pdb=" O3A ATP 3 901 " pdb=" PB ATP 3 901 " ideal model delta sigma weight residual 136.83 118.33 18.50 1.00e+00 1.00e+00 3.42e+02 ... (remaining 56497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 24545 34.93 - 69.86: 883 69.86 - 104.79: 71 104.79 - 139.72: 3 139.72 - 174.65: 1 Dihedral angle restraints: 25503 sinusoidal: 10698 harmonic: 14805 Sorted by residual: dihedral pdb=" CA ASP 7 382 " pdb=" C ASP 7 382 " pdb=" N PRO 7 383 " pdb=" CA PRO 7 383 " ideal model delta harmonic sigma weight residual -180.00 -119.40 -60.60 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 133.21 46.79 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA ILE 4 615 " pdb=" C ILE 4 615 " pdb=" N LEU 4 616 " pdb=" CA LEU 4 616 " ideal model delta harmonic sigma weight residual 180.00 136.47 43.53 0 5.00e+00 4.00e-02 7.58e+01 ... (remaining 25500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.584: 6338 0.584 - 1.169: 3 1.169 - 1.753: 17 1.753 - 2.338: 3 2.338 - 2.922: 1 Chirality restraints: 6362 Sorted by residual: chirality pdb=" CB VAL 5 432 " pdb=" CA VAL 5 432 " pdb=" CG1 VAL 5 432 " pdb=" CG2 VAL 5 432 " both_signs ideal model delta sigma weight residual False -2.63 0.29 -2.92 2.00e-01 2.50e+01 2.14e+02 chirality pdb=" CB ILE 2 585 " pdb=" CA ILE 2 585 " pdb=" CG1 ILE 2 585 " pdb=" CG2 ILE 2 585 " both_signs ideal model delta sigma weight residual False 2.64 0.66 1.99 2.00e-01 2.50e+01 9.89e+01 chirality pdb=" CB VAL 2 463 " pdb=" CA VAL 2 463 " pdb=" CG1 VAL 2 463 " pdb=" CG2 VAL 2 463 " both_signs ideal model delta sigma weight residual False -2.63 -0.68 -1.95 2.00e-01 2.50e+01 9.50e+01 ... (remaining 6359 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 521 " -0.425 9.50e-02 1.11e+02 2.21e-01 1.78e+02 pdb=" NE ARG 6 521 " 0.105 2.00e-02 2.50e+03 pdb=" CZ ARG 6 521 " -0.210 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 521 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 521 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 5 199 " -0.100 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO 5 200 " 0.264 5.00e-02 4.00e+02 pdb=" CA PRO 5 200 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO 5 200 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 4 513 " -0.082 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO 4 514 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO 4 514 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO 4 514 " -0.066 5.00e-02 4.00e+02 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 8 2.03 - 2.74: 6178 2.74 - 3.46: 64294 3.46 - 4.18: 98792 4.18 - 4.90: 160235 Nonbonded interactions: 329507 Sorted by model distance: nonbonded pdb=" OG SER 3 347 " pdb=" O1B ATP 3 901 " model vdw 1.308 2.440 nonbonded pdb=" CB SER 3 347 " pdb=" O1B ATP 3 901 " model vdw 1.373 3.440 nonbonded pdb=" O ILE A 237 " pdb=" OG1 THR A 241 " model vdw 1.971 2.440 nonbonded pdb=" O GLU 2 278 " pdb=" OG1 THR 2 281 " model vdw 1.998 2.440 nonbonded pdb=" O GLU L 90 " pdb=" OG1 THR L 149 " model vdw 2.002 2.440 ... (remaining 329502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 239 5.16 5 C 25619 2.51 5 N 7193 2.21 5 O 7875 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 5.140 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: 0.040 Extract box with map and model: 19.020 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.000 Process input model: 99.860 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 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 : 0.011 0.158 41733 Z= 0.749 Angle : 1.458 27.476 56502 Z= 0.798 Chirality : 0.127 2.922 6362 Planarity : 0.009 0.221 7230 Dihedral : 18.031 174.646 15884 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 19.24 % Favored : 80.28 % Rotamer Outliers : 6.70 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.95 % 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: -5.61 (0.09), residues: 5000 helix: -3.27 (0.09), residues: 1545 sheet: -4.59 (0.15), residues: 465 loop : -4.03 (0.10), residues: 2990 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 961 time to evaluate : 5.098 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 297 outliers final: 121 residues processed: 1214 average time/residue: 0.5396 time to fit residues: 1041.0092 Evaluate side-chains 732 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 611 time to evaluate : 4.484 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 121 outliers final: 3 residues processed: 121 average time/residue: 0.3512 time to fit residues: 87.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 423 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 393 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 292 optimal weight: 7.9990 chunk 455 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 267 HIS 2 352 GLN 2 390 GLN 2 412 ASN 2 534 GLN 2 548 ASN 2 592 GLN 2 631 ASN 2 659 GLN 2 666 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 694 GLN 2 699 GLN 2 762 ASN 3 13 GLN 3 57 GLN 3 233 GLN 3 288 ASN 3 434 HIS 3 448 ASN 3 495 HIS 3 504 ASN 3 551 GLN 3 605 GLN 4 182 GLN 4 214 ASN 4 260 GLN 4 267 ASN 4 326 ASN 4 344 HIS ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 358 GLN 4 372 ASN 4 378 HIS ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 520 GLN 4 527 ASN 4 627 ASN 4 699 HIS ** 4 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 735 GLN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN 5 334 GLN 5 373 ASN ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 462 GLN 5 486 ASN 5 532 HIS ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 644 GLN 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN ** 6 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 296 GLN ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 533 ASN 6 612 GLN 7 42 HIS 7 214 ASN 7 347 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 453 GLN ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 522 GLN A 154 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 467 HIS A 508 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 HIS ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 91 HIS ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 HIS N 164 GLN N 214 GLN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 41733 Z= 0.260 Angle : 0.866 15.791 56502 Z= 0.442 Chirality : 0.049 0.210 6362 Planarity : 0.007 0.115 7230 Dihedral : 11.555 141.351 5873 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.38 % Favored : 86.60 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.10), residues: 5000 helix: -2.17 (0.11), residues: 1573 sheet: -3.86 (0.17), residues: 520 loop : -3.61 (0.10), residues: 2907 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 755 time to evaluate : 4.630 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 180 outliers final: 75 residues processed: 882 average time/residue: 0.5547 time to fit residues: 785.0676 Evaluate side-chains 657 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 582 time to evaluate : 4.799 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 75 outliers final: 4 residues processed: 75 average time/residue: 0.3730 time to fit residues: 58.7348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 253 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 379 optimal weight: 4.9990 chunk 310 optimal weight: 0.0980 chunk 125 optimal weight: 0.9990 chunk 456 optimal weight: 0.9980 chunk 493 optimal weight: 1.9990 chunk 406 optimal weight: 5.9990 chunk 452 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 366 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 210 GLN 2 267 HIS ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 783 GLN 3 423 GLN 3 438 ASN 3 567 HIS 4 353 GLN ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 120 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 241 GLN ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN 7 453 GLN ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 77 ASN H 121 ASN ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 41733 Z= 0.221 Angle : 0.762 11.563 56502 Z= 0.387 Chirality : 0.046 0.216 6362 Planarity : 0.006 0.122 7230 Dihedral : 11.003 141.979 5873 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.80 % Favored : 86.18 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.06 % 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: -4.14 (0.10), residues: 5000 helix: -1.70 (0.12), residues: 1593 sheet: -3.42 (0.18), residues: 515 loop : -3.39 (0.10), residues: 2892 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 665 time to evaluate : 5.418 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 156 outliers final: 66 residues processed: 780 average time/residue: 0.5502 time to fit residues: 690.1540 Evaluate side-chains 644 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 578 time to evaluate : 5.075 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 66 outliers final: 4 residues processed: 66 average time/residue: 0.3853 time to fit residues: 54.3062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 451 optimal weight: 5.9990 chunk 343 optimal weight: 0.0070 chunk 237 optimal weight: 0.0060 chunk 50 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 458 optimal weight: 6.9990 chunk 485 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 434 optimal weight: 5.9990 chunk 130 optimal weight: 0.0980 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 436 GLN 2 658 GLN 2 754 HIS ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 386 GLN ** 4 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 677 HIS ** 4 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 486 ASN 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 203 GLN ** 6 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 466 HIS 6 496 ASN 6 584 HIS 7 248 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN H 68 ASN H 120 ASN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 41733 Z= 0.196 Angle : 0.727 13.501 56502 Z= 0.364 Chirality : 0.045 0.194 6362 Planarity : 0.005 0.122 7230 Dihedral : 10.589 151.548 5873 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.08 % Favored : 87.90 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.11), residues: 5000 helix: -1.41 (0.12), residues: 1595 sheet: -3.24 (0.19), residues: 523 loop : -3.23 (0.10), residues: 2882 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 661 time to evaluate : 5.057 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 136 outliers final: 62 residues processed: 756 average time/residue: 0.5494 time to fit residues: 671.9770 Evaluate side-chains 620 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 558 time to evaluate : 4.845 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 62 outliers final: 4 residues processed: 62 average time/residue: 0.3895 time to fit residues: 51.2942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 404 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 414 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 435 optimal weight: 0.9990 chunk 122 optimal weight: 0.0470 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 211 ASN ** 2 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 503 ASN 2 658 GLN ** 2 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 672 HIS 2 754 HIS 2 758 HIS 3 143 HIS ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN 3 567 HIS 3 605 GLN 4 188 ASN ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 337 ASN ** 4 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 620 ASN 4 656 GLN 4 735 GLN ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 635 HIS 6 90 ASN 6 115 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 165 GLN ** 6 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 646 GLN ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS M 151 ASN M 164 ASN N 36 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.139 41733 Z= 0.297 Angle : 0.823 14.579 56502 Z= 0.417 Chirality : 0.048 0.243 6362 Planarity : 0.006 0.134 7230 Dihedral : 10.738 152.304 5873 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.30 % Favored : 85.68 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.11), residues: 5000 helix: -1.39 (0.12), residues: 1613 sheet: -3.10 (0.19), residues: 497 loop : -3.24 (0.10), residues: 2890 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 639 time to evaluate : 4.801 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 163 outliers final: 86 residues processed: 752 average time/residue: 0.5509 time to fit residues: 671.8543 Evaluate side-chains 652 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 566 time to evaluate : 5.010 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 86 outliers final: 4 residues processed: 86 average time/residue: 0.3729 time to fit residues: 67.1850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 163 optimal weight: 4.9990 chunk 436 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 284 optimal weight: 0.2980 chunk 119 optimal weight: 7.9990 chunk 485 optimal weight: 0.0770 chunk 403 optimal weight: 0.9990 chunk 224 optimal weight: 0.0040 chunk 40 optimal weight: 0.6980 chunk 160 optimal weight: 0.3980 chunk 254 optimal weight: 2.9990 overall best weight: 0.2950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 590 HIS 4 620 ASN 5 21 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 635 HIS 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 GLN 6 396 GLN 7 42 HIS 7 105 HIS ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS A 262 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 487 HIS H 121 ASN ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 HIS ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 172 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.195 41733 Z= 0.225 Angle : 0.739 12.975 56502 Z= 0.370 Chirality : 0.044 0.220 6362 Planarity : 0.005 0.136 7230 Dihedral : 10.331 156.003 5873 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.48 % Favored : 88.50 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.11), residues: 5000 helix: -1.15 (0.13), residues: 1603 sheet: -2.86 (0.20), residues: 518 loop : -3.10 (0.10), residues: 2879 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 642 time to evaluate : 4.610 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 96 outliers final: 51 residues processed: 709 average time/residue: 0.5532 time to fit residues: 639.0143 Evaluate side-chains 607 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 556 time to evaluate : 4.737 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 51 outliers final: 4 residues processed: 51 average time/residue: 0.3882 time to fit residues: 42.8191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 468 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 354 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 chunk 408 optimal weight: 0.9980 chunk 271 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 294 optimal weight: 0.3980 chunk 223 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 620 ASN 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 461 GLN 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 231 GLN 6 595 GLN ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 376 ASN ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN A 101 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.133 41733 Z= 0.228 Angle : 0.741 13.361 56502 Z= 0.372 Chirality : 0.045 0.210 6362 Planarity : 0.006 0.118 7230 Dihedral : 10.261 153.772 5873 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.84 % Favored : 87.14 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.11), residues: 5000 helix: -1.12 (0.13), residues: 1630 sheet: -2.80 (0.20), residues: 527 loop : -3.05 (0.11), residues: 2843 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 602 time to evaluate : 4.898 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 83 outliers final: 42 residues processed: 652 average time/residue: 0.5499 time to fit residues: 583.7854 Evaluate side-chains 602 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 560 time to evaluate : 4.953 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 42 outliers final: 4 residues processed: 42 average time/residue: 0.4737 time to fit residues: 42.1834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 299 optimal weight: 0.1980 chunk 193 optimal weight: 0.0170 chunk 288 optimal weight: 0.3980 chunk 145 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 307 optimal weight: 0.8980 chunk 329 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 635 HIS 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 564 ASN ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN H 182 HIS ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.195 41733 Z= 0.223 Angle : 0.730 13.563 56502 Z= 0.365 Chirality : 0.044 0.197 6362 Planarity : 0.006 0.159 7230 Dihedral : 10.045 146.820 5873 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.20 % Favored : 88.78 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.11), residues: 5000 helix: -0.96 (0.13), residues: 1616 sheet: -2.67 (0.20), residues: 516 loop : -2.97 (0.11), residues: 2868 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 614 time to evaluate : 5.498 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 55 outliers final: 31 residues processed: 649 average time/residue: 0.5598 time to fit residues: 586.9055 Evaluate side-chains 600 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 569 time to evaluate : 4.900 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 31 outliers final: 4 residues processed: 31 average time/residue: 0.3744 time to fit residues: 28.8426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 440 optimal weight: 0.6980 chunk 463 optimal weight: 0.4980 chunk 422 optimal weight: 2.9990 chunk 450 optimal weight: 3.9990 chunk 271 optimal weight: 0.2980 chunk 196 optimal weight: 0.0370 chunk 354 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 407 optimal weight: 0.9980 chunk 426 optimal weight: 0.9990 chunk 449 optimal weight: 0.3980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 329 ASN ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 231 GLN ** 6 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 HIS ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.141 41733 Z= 0.199 Angle : 0.721 13.023 56502 Z= 0.359 Chirality : 0.044 0.231 6362 Planarity : 0.006 0.167 7230 Dihedral : 9.877 135.653 5873 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.60 % Favored : 88.38 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.11), residues: 5000 helix: -0.85 (0.13), residues: 1605 sheet: -2.56 (0.21), residues: 518 loop : -2.92 (0.11), residues: 2877 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 615 time to evaluate : 4.828 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 31 outliers final: 15 residues processed: 633 average time/residue: 0.5664 time to fit residues: 583.7714 Evaluate side-chains 594 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 579 time to evaluate : 4.892 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 4 residues processed: 15 average time/residue: 0.3626 time to fit residues: 17.6423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 296 optimal weight: 2.9990 chunk 476 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 500 optimal weight: 0.0770 chunk 460 optimal weight: 0.9990 chunk 398 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 307 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 206 GLN ** 7 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS A 296 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.6918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.193 41733 Z= 0.243 Angle : 0.755 17.727 56502 Z= 0.380 Chirality : 0.044 0.249 6362 Planarity : 0.006 0.185 7230 Dihedral : 9.828 134.868 5873 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.14 % Favored : 87.84 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.14 (0.11), residues: 5000 helix: -0.81 (0.13), residues: 1586 sheet: -2.42 (0.21), residues: 516 loop : -2.90 (0.11), residues: 2898 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 605 time to evaluate : 4.831 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 TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR 7 88 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 24 outliers final: 17 residues processed: 614 average time/residue: 0.5685 time to fit residues: 567.1265 Evaluate side-chains 600 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 583 time to evaluate : 5.031 Switching outliers to nearest non-outliers revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 4 residues processed: 17 average time/residue: 0.4012 time to fit residues: 19.9597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 316 optimal weight: 0.9990 chunk 424 optimal weight: 0.0870 chunk 122 optimal weight: 0.0970 chunk 367 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 398 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 409 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 105 ASN ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 115 HIS ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 564 ASN ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.273304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.259491 restraints weight = 73905.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.259184 restraints weight = 98234.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.260061 restraints weight = 83322.176| |-----------------------------------------------------------------------------| r_work (final): 0.5044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5461 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.726 41733 Z= 0.389 Angle : 0.768 26.789 56502 Z= 0.390 Chirality : 0.044 0.321 6362 Planarity : 0.006 0.183 7230 Dihedral : 9.733 134.367 5873 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.68 % Favored : 88.30 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.11), residues: 5000 helix: -0.75 (0.13), residues: 1575 sheet: -2.38 (0.21), residues: 529 loop : -2.83 (0.11), residues: 2896 =============================================================================== Job complete usr+sys time: 10840.15 seconds wall clock time: 197 minutes 14.34 seconds (11834.34 seconds total)