Starting phenix.real_space_refine on Sun Mar 24 10:04:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/03_2024/6rax_4786_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/03_2024/6rax_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_4786/03_2024/6rax_4786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/03_2024/6rax_4786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/03_2024/6rax_4786_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rax_4786/03_2024/6rax_4786_updated.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 4} 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: 21.03, 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: 17.34 Conformation dependent library (CDL) restraints added in 7.4 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: 9.03 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: 13.25 Time building geometry restraints manager: 18.28 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: 24623 34.93 - 69.86: 910 69.86 - 104.79: 75 104.79 - 139.72: 3 139.72 - 174.65: 1 Dihedral angle restraints: 25612 sinusoidal: 10807 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 25609 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 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.710 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 106.550 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5632 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 : 18.186 174.646 15993 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.48 % Allowed : 19.24 % Favored : 80.28 % Rotamer: Outliers : 6.70 % Allowed : 15.27 % Favored : 78.03 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP M 170 HIS 0.020 0.004 HIS M 115 PHE 0.041 0.005 PHE M 17 TYR 0.063 0.004 TYR N 104 ARG 0.215 0.003 ARG 6 521 *********************** 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 : 4.206 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. REVERT: 2 212 MET cc_start: 0.7591 (mmp) cc_final: 0.5610 (ttp) REVERT: 2 271 SER cc_start: 0.5576 (OUTLIER) cc_final: 0.5199 (t) REVERT: 2 284 LYS cc_start: 0.6311 (pptt) cc_final: 0.5987 (tttm) REVERT: 2 553 GLU cc_start: 0.6522 (mp0) cc_final: 0.5208 (tp30) REVERT: 2 568 VAL cc_start: 0.4054 (OUTLIER) cc_final: 0.3693 (p) REVERT: 2 626 MET cc_start: -0.0253 (ttt) cc_final: -0.0504 (mtt) REVERT: 2 666 HIS cc_start: 0.8439 (t70) cc_final: 0.8231 (t70) REVERT: 2 722 LYS cc_start: 0.6548 (mptt) cc_final: 0.6282 (ptmm) REVERT: 2 752 GLU cc_start: 0.6432 (pt0) cc_final: 0.5847 (pt0) REVERT: 3 85 ASP cc_start: 0.8161 (t0) cc_final: 0.7773 (t0) REVERT: 3 221 ASP cc_start: 0.6922 (m-30) cc_final: 0.6636 (t0) REVERT: 3 226 CYS cc_start: 0.3352 (t) cc_final: 0.3119 (t) REVERT: 3 265 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7022 (pp) REVERT: 3 296 LYS cc_start: 0.6419 (mttt) cc_final: 0.5854 (pttt) REVERT: 3 348 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.4223 (tp40) REVERT: 3 458 LYS cc_start: 0.6945 (tmmt) cc_final: 0.5784 (mmmt) REVERT: 3 470 LEU cc_start: 0.5901 (mp) cc_final: 0.5260 (pp) REVERT: 3 525 PHE cc_start: 0.5387 (m-10) cc_final: 0.5039 (m-80) REVERT: 3 572 MET cc_start: 0.7074 (mmp) cc_final: 0.6653 (mmp) REVERT: 3 641 GLU cc_start: 0.5762 (mt-10) cc_final: 0.5012 (tp30) REVERT: 4 188 ASN cc_start: 0.6025 (m-40) cc_final: 0.5664 (p0) REVERT: 4 193 GLN cc_start: 0.5552 (tt0) cc_final: 0.5059 (tm-30) REVERT: 4 278 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (m-40) REVERT: 4 424 PHE cc_start: 0.6929 (m-80) cc_final: 0.6704 (m-80) REVERT: 4 558 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5592 (mm) REVERT: 4 590 HIS cc_start: 0.5073 (OUTLIER) cc_final: 0.4064 (m170) REVERT: 4 595 GLN cc_start: 0.8242 (mt0) cc_final: 0.7129 (mm-40) REVERT: 4 645 ARG cc_start: 0.2379 (OUTLIER) cc_final: 0.2095 (tmt-80) REVERT: 4 647 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: 4 653 LEU cc_start: 0.4993 (pt) cc_final: 0.4384 (tp) REVERT: 4 676 ARG cc_start: 0.3033 (pmt-80) cc_final: 0.1451 (ppt170) REVERT: 4 680 GLU cc_start: 0.1557 (pm20) cc_final: 0.0396 (mt-10) REVERT: 5 68 GLU cc_start: 0.5551 (pt0) cc_final: 0.5121 (pt0) REVERT: 5 71 ASP cc_start: 0.7275 (p0) cc_final: 0.6868 (p0) REVERT: 5 216 CYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6295 (p) REVERT: 5 239 HIS cc_start: 0.7775 (p90) cc_final: 0.7571 (p-80) REVERT: 5 241 GLN cc_start: 0.4793 (pt0) cc_final: 0.4508 (mm-40) REVERT: 5 257 ARG cc_start: 0.6559 (mtm180) cc_final: 0.6068 (ptp-110) REVERT: 5 307 ARG cc_start: 0.5655 (OUTLIER) cc_final: 0.5137 (pmt170) REVERT: 5 360 LYS cc_start: 0.3016 (mmtt) cc_final: 0.2658 (mmtp) REVERT: 5 379 ASP cc_start: 0.7075 (t0) cc_final: 0.6691 (t0) REVERT: 5 402 SER cc_start: 0.6943 (OUTLIER) cc_final: 0.6696 (t) REVERT: 5 417 LYS cc_start: 0.7944 (pttt) cc_final: 0.7023 (mppt) REVERT: 5 443 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: 5 514 ILE cc_start: 0.4010 (mp) cc_final: 0.3768 (mp) REVERT: 5 588 MET cc_start: 0.6800 (tpp) cc_final: 0.5673 (tpp) REVERT: 5 641 ARG cc_start: 0.6202 (mmt180) cc_final: 0.5980 (mmm160) REVERT: 6 16 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6158 (tp30) REVERT: 6 55 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5032 (pt) REVERT: 6 90 ASN cc_start: 0.7782 (m110) cc_final: 0.7528 (m-40) REVERT: 6 116 LYS cc_start: 0.5981 (mmtt) cc_final: 0.5597 (ttmm) REVERT: 6 220 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6477 (mm) REVERT: 6 284 LEU cc_start: 0.2619 (OUTLIER) cc_final: 0.2226 (pp) REVERT: 6 296 GLN cc_start: 0.7603 (tp-100) cc_final: 0.6713 (tt0) REVERT: 6 309 MET cc_start: 0.2657 (mtp) cc_final: 0.1376 (tmm) REVERT: 6 325 GLU cc_start: 0.6290 (mp0) cc_final: 0.5212 (mp0) REVERT: 6 332 MET cc_start: 0.4115 (mpp) cc_final: 0.2237 (tpt) REVERT: 6 410 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.3111 (t80) REVERT: 6 537 ASP cc_start: 0.7255 (m-30) cc_final: 0.6939 (m-30) REVERT: 6 612 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7134 (mt0) REVERT: 6 639 GLU cc_start: 0.4315 (tt0) cc_final: 0.4033 (mt-10) REVERT: 7 57 GLU cc_start: 0.6852 (tt0) cc_final: 0.6315 (mp0) REVERT: 7 83 GLU cc_start: 0.5046 (mm-30) cc_final: 0.3981 (tp30) REVERT: 7 131 MET cc_start: 0.6273 (ptm) cc_final: 0.5900 (tmm) REVERT: 7 223 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8443 (tp-100) REVERT: 7 281 MET cc_start: 0.7784 (mtm) cc_final: 0.7117 (mtp) REVERT: 7 282 ARG cc_start: 0.6986 (tmt-80) cc_final: 0.5896 (ttm-80) REVERT: 7 419 MET cc_start: -0.4666 (ttp) cc_final: -0.5332 (mmt) REVERT: 7 494 ARG cc_start: 0.3790 (ptm-80) cc_final: 0.2558 (ttm170) REVERT: 7 527 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6026 (mmt180) REVERT: 7 536 HIS cc_start: 0.5355 (m90) cc_final: 0.5081 (m-70) REVERT: 7 556 MET cc_start: 0.2602 (ptm) cc_final: 0.1666 (tmm) REVERT: 7 589 ARG cc_start: 0.7278 (mtp180) cc_final: 0.6991 (mtp85) REVERT: 7 634 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5874 (mt) REVERT: 7 635 ARG cc_start: 0.6370 (ptm-80) cc_final: 0.6074 (tpp-160) REVERT: A 53 MET cc_start: 0.4975 (mpp) cc_final: 0.4127 (ttp) REVERT: A 65 HIS cc_start: 0.8701 (m90) cc_final: 0.8426 (m170) REVERT: A 223 TRP cc_start: 0.6285 (t60) cc_final: 0.5816 (t60) REVERT: A 460 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7644 (t80) REVERT: A 567 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5597 (tt) REVERT: H 16 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2668 (mp) REVERT: H 70 ARG cc_start: 0.7774 (tmm160) cc_final: 0.7324 (tmm160) REVERT: H 88 ARG cc_start: 0.6762 (mmt180) cc_final: 0.5624 (mmt180) REVERT: L 119 ASP cc_start: 0.7719 (t70) cc_final: 0.7510 (t0) REVERT: N 60 THR cc_start: 0.7518 (p) cc_final: 0.7059 (m) REVERT: N 107 CYS cc_start: 0.5726 (OUTLIER) cc_final: 0.4463 (m) REVERT: N 151 TYR cc_start: 0.4065 (t80) cc_final: 0.3626 (t80) outliers start: 297 outliers final: 120 residues processed: 1214 average time/residue: 0.5889 time to fit residues: 1145.3036 Evaluate side-chains 785 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 642 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 271 SER Chi-restraints excluded: chain 2 residue 307 LEU Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 381 VAL Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 423 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 442 THR Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 518 LEU Chi-restraints excluded: chain 2 residue 531 THR Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 565 ASP Chi-restraints excluded: chain 2 residue 568 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 605 LEU Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 727 LEU Chi-restraints excluded: chain 2 residue 743 HIS Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 3 residue 33 VAL Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 214 VAL Chi-restraints excluded: chain 3 residue 256 VAL Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 301 SER Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 341 ASP Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 374 THR Chi-restraints excluded: chain 3 residue 400 VAL Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 4 residue 237 ILE Chi-restraints excluded: chain 4 residue 276 SER Chi-restraints excluded: chain 4 residue 278 ASN Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 510 LEU Chi-restraints excluded: chain 4 residue 516 THR Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 4 residue 558 LEU Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 4 residue 638 LEU Chi-restraints excluded: chain 4 residue 645 ARG Chi-restraints excluded: chain 4 residue 647 ASP Chi-restraints excluded: chain 4 residue 740 ILE Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 137 SER Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 253 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 313 SER Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 387 LEU Chi-restraints excluded: chain 5 residue 402 SER Chi-restraints excluded: chain 5 residue 441 ILE Chi-restraints excluded: chain 5 residue 443 GLU Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 464 ILE Chi-restraints excluded: chain 5 residue 502 ASP Chi-restraints excluded: chain 5 residue 536 VAL Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 398 LEU Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 451 ILE Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 6 residue 612 GLN Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 173 VAL Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 269 ASP Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 356 LEU Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 484 ILE Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 634 LEU Chi-restraints excluded: chain 7 residue 644 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 CYS Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 110 CYS Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 423 optimal weight: 0.8980 chunk 380 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 129 optimal weight: 0.0970 chunk 256 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 393 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 chunk 292 optimal weight: 7.9990 chunk 455 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 2 671 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 3 288 ASN 3 434 HIS 3 448 ASN 3 495 HIS 3 504 ASN 3 551 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 378 HIS 4 485 GLN 4 527 ASN 4 620 ASN 4 627 ASN 4 699 HIS ** 4 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 735 GLN 5 120 GLN ** 5 134 GLN ** 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 ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 198 GLN ** 6 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 533 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 7 645 ASN A 154 HIS A 296 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS A 436 HIS A 467 HIS A 508 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41733 Z= 0.237 Angle : 0.830 12.515 56502 Z= 0.423 Chirality : 0.049 0.268 6362 Planarity : 0.006 0.095 7230 Dihedral : 13.347 141.858 6220 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.28 % Favored : 86.70 % Rotamer: Outliers : 5.21 % Allowed : 19.58 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.10), residues: 5000 helix: -2.13 (0.11), residues: 1582 sheet: -3.84 (0.18), residues: 493 loop : -3.58 (0.10), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 193 HIS 0.012 0.001 HIS N 153 PHE 0.030 0.002 PHE 5 47 TYR 0.031 0.002 TYR 4 196 ARG 0.010 0.001 ARG 6 521 *********************** 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 1006 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 775 time to evaluate : 4.736 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 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 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 revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. REVERT: 2 279 LEU cc_start: 0.8023 (tp) cc_final: 0.7753 (tp) REVERT: 2 284 LYS cc_start: 0.6340 (pptt) cc_final: 0.6000 (ttpt) REVERT: 2 340 CYS cc_start: 0.8690 (m) cc_final: 0.8260 (p) REVERT: 2 488 GLU cc_start: 0.6470 (mm-30) cc_final: 0.5550 (mm-30) REVERT: 2 553 GLU cc_start: 0.6366 (mp0) cc_final: 0.5438 (tp30) REVERT: 2 605 LEU cc_start: 0.7260 (tp) cc_final: 0.6771 (tp) REVERT: 2 626 MET cc_start: -0.1022 (ttt) cc_final: -0.1432 (mtt) REVERT: 2 744 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6313 (mm) REVERT: 2 752 GLU cc_start: 0.5906 (pt0) cc_final: 0.5365 (pt0) REVERT: 2 789 LYS cc_start: 0.4573 (OUTLIER) cc_final: 0.4047 (ttpp) REVERT: 3 36 MET cc_start: 0.5438 (mmp) cc_final: 0.4986 (ttm) REVERT: 3 58 ARG cc_start: 0.6490 (mmp80) cc_final: 0.6056 (mmt180) REVERT: 3 155 LYS cc_start: 0.6434 (ttmt) cc_final: 0.6187 (tptp) REVERT: 3 190 TYR cc_start: 0.5174 (p90) cc_final: 0.4631 (p90) REVERT: 3 218 CYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8174 (t) REVERT: 3 253 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6165 (t80) REVERT: 3 296 LYS cc_start: 0.6111 (mttt) cc_final: 0.5599 (pttt) REVERT: 3 364 THR cc_start: 0.5686 (OUTLIER) cc_final: 0.5186 (p) REVERT: 3 458 LYS cc_start: 0.7178 (tmmt) cc_final: 0.5934 (mmmt) REVERT: 3 462 GLU cc_start: 0.8425 (tp30) cc_final: 0.7620 (tp30) REVERT: 3 470 LEU cc_start: 0.6027 (mp) cc_final: 0.5284 (pp) REVERT: 3 479 VAL cc_start: 0.3624 (t) cc_final: 0.2926 (p) REVERT: 3 482 ASP cc_start: 0.5412 (t0) cc_final: 0.5198 (t0) REVERT: 3 562 MET cc_start: 0.6232 (tmm) cc_final: 0.5897 (ttm) REVERT: 3 563 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7142 (ttp80) REVERT: 3 624 ARG cc_start: 0.4646 (OUTLIER) cc_final: 0.4244 (ptp-110) REVERT: 4 188 ASN cc_start: 0.6250 (m-40) cc_final: 0.5885 (p0) REVERT: 4 193 GLN cc_start: 0.5660 (tt0) cc_final: 0.5139 (tm-30) REVERT: 4 211 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7206 (tp) REVERT: 4 291 MET cc_start: -0.0541 (mtm) cc_final: -0.0832 (ttp) REVERT: 4 524 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: 4 593 MET cc_start: 0.4949 (mtm) cc_final: 0.3258 (tmm) REVERT: 4 630 LYS cc_start: 0.7855 (tttm) cc_final: 0.7557 (mmtm) REVERT: 4 647 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6225 (m-30) REVERT: 4 653 LEU cc_start: 0.5288 (pt) cc_final: 0.4783 (tp) REVERT: 4 680 GLU cc_start: 0.1507 (pm20) cc_final: 0.0428 (mt-10) REVERT: 4 695 TYR cc_start: 0.8754 (t80) cc_final: 0.8465 (t80) REVERT: 5 216 CYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6705 (p) REVERT: 5 239 HIS cc_start: 0.7634 (p90) cc_final: 0.7319 (p90) REVERT: 5 240 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6413 (tp) REVERT: 5 245 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6214 (t0) REVERT: 5 330 GLU cc_start: 0.5745 (tp30) cc_final: 0.5382 (tp30) REVERT: 5 360 LYS cc_start: 0.2880 (mmtt) cc_final: 0.2383 (mmtp) REVERT: 5 379 ASP cc_start: 0.6903 (t0) cc_final: 0.6423 (t0) REVERT: 5 402 SER cc_start: 0.7307 (OUTLIER) cc_final: 0.6918 (t) REVERT: 5 416 MET cc_start: 0.7390 (ppp) cc_final: 0.7101 (ppp) REVERT: 5 417 LYS cc_start: 0.7917 (pttt) cc_final: 0.6820 (mttp) REVERT: 5 641 ARG cc_start: 0.6405 (mmt180) cc_final: 0.6125 (mmm160) REVERT: 6 16 GLU cc_start: 0.6242 (mm-30) cc_final: 0.6017 (tp30) REVERT: 6 55 LEU cc_start: 0.5541 (tt) cc_final: 0.5098 (pt) REVERT: 6 116 LYS cc_start: 0.6120 (mmtt) cc_final: 0.5759 (ttmm) REVERT: 6 198 GLN cc_start: 0.7331 (pt0) cc_final: 0.6330 (pm20) REVERT: 6 219 GLU cc_start: 0.6160 (mp0) cc_final: 0.5784 (mp0) REVERT: 6 284 LEU cc_start: 0.2895 (OUTLIER) cc_final: 0.2369 (pp) REVERT: 6 288 MET cc_start: 0.7684 (tmm) cc_final: 0.7334 (tmm) REVERT: 6 296 GLN cc_start: 0.7675 (tp-100) cc_final: 0.6785 (tt0) REVERT: 6 309 MET cc_start: 0.3186 (mtp) cc_final: 0.1316 (tmm) REVERT: 6 332 MET cc_start: 0.4175 (mpp) cc_final: 0.2595 (tpt) REVERT: 6 410 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.3830 (t80) REVERT: 6 637 VAL cc_start: 0.8060 (p) cc_final: 0.7854 (p) REVERT: 7 83 GLU cc_start: 0.5195 (mm-30) cc_final: 0.4785 (pp20) REVERT: 7 150 ARG cc_start: 0.7166 (ptm-80) cc_final: 0.6820 (ptm-80) REVERT: 7 215 LYS cc_start: 0.3053 (OUTLIER) cc_final: 0.1566 (tttp) REVERT: 7 248 HIS cc_start: 0.7298 (t70) cc_final: 0.7092 (t70) REVERT: 7 256 MET cc_start: 0.7841 (tmm) cc_final: 0.6622 (mmm) REVERT: 7 281 MET cc_start: 0.7690 (mtm) cc_final: 0.6996 (mtp) REVERT: 7 282 ARG cc_start: 0.7343 (tmt-80) cc_final: 0.6127 (ttm-80) REVERT: 7 294 SER cc_start: 0.6695 (OUTLIER) cc_final: 0.6357 (p) REVERT: 7 391 LEU cc_start: 0.8664 (tp) cc_final: 0.8187 (tp) REVERT: 7 419 MET cc_start: -0.5343 (ttp) cc_final: -0.5645 (mmt) REVERT: 7 438 ASP cc_start: 0.5212 (p0) cc_final: 0.4791 (p0) REVERT: 7 453 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7391 (pp30) REVERT: 7 494 ARG cc_start: 0.4151 (ptm-80) cc_final: 0.2970 (ttm170) REVERT: 7 527 ARG cc_start: 0.7339 (ttp80) cc_final: 0.6318 (mmt180) REVERT: 7 556 MET cc_start: 0.2220 (ptm) cc_final: 0.1541 (ttp) REVERT: 7 589 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6942 (mtp85) REVERT: 7 635 ARG cc_start: 0.6372 (ptm-80) cc_final: 0.5938 (mmt180) REVERT: A 18 ARG cc_start: 0.6780 (ptp90) cc_final: 0.6546 (ptp90) REVERT: A 53 MET cc_start: 0.5325 (mpp) cc_final: 0.4258 (mtm) REVERT: A 115 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7640 (m) REVERT: A 342 TYR cc_start: 0.5601 (t80) cc_final: 0.5346 (t80) REVERT: A 467 HIS cc_start: 0.5042 (OUTLIER) cc_final: 0.4823 (m90) REVERT: H 80 CYS cc_start: 0.7246 (t) cc_final: 0.6675 (t) REVERT: H 88 ARG cc_start: 0.6615 (mmt180) cc_final: 0.6102 (ttp80) REVERT: L 120 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7873 (mm) REVERT: L 151 LEU cc_start: 0.7180 (mp) cc_final: 0.6972 (tp) REVERT: M 101 PHE cc_start: 0.4727 (t80) cc_final: 0.4438 (t80) REVERT: M 123 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8087 (mm-30) REVERT: N 114 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6157 (m) REVERT: N 151 TYR cc_start: 0.4052 (t80) cc_final: 0.3545 (t80) outliers start: 231 outliers final: 108 residues processed: 950 average time/residue: 0.5433 time to fit residues: 822.1839 Evaluate side-chains 758 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 628 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 506 ILE Chi-restraints excluded: chain 2 residue 532 THR Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 789 LYS Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 199 GLN Chi-restraints excluded: chain 3 residue 218 CYS Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 528 SER Chi-restraints excluded: chain 3 residue 624 ARG Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 331 CYS Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 510 LEU Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 647 ASP Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 685 ASP Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 402 SER Chi-restraints excluded: chain 5 residue 463 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 281 MET Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 335 ASP Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 294 SER Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 350 VAL Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 421 ASP Chi-restraints excluded: chain 7 residue 453 GLN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 253 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 379 optimal weight: 3.9990 chunk 310 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 456 optimal weight: 0.9990 chunk 493 optimal weight: 0.7980 chunk 406 optimal weight: 5.9990 chunk 452 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 366 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 659 GLN 2 666 HIS ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 233 GLN ** 3 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 GLN 3 438 ASN 3 567 HIS 4 353 GLN 4 358 GLN 4 372 ASN 4 520 GLN ** 4 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 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** 6 90 ASN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 203 GLN ** 6 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 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** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN H 109 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 GLN ** N 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41733 Z= 0.210 Angle : 0.747 11.473 56502 Z= 0.380 Chirality : 0.046 0.208 6362 Planarity : 0.006 0.073 7230 Dihedral : 12.408 144.751 6078 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.70 % Favored : 86.26 % Rotamer: Outliers : 5.55 % Allowed : 21.93 % Favored : 72.52 % 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: -4.11 (0.10), residues: 5000 helix: -1.65 (0.12), residues: 1598 sheet: -3.43 (0.18), residues: 521 loop : -3.38 (0.10), residues: 2881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 170 HIS 0.021 0.001 HIS A 467 PHE 0.022 0.002 PHE 4 424 TYR 0.023 0.002 TYR 4 196 ARG 0.020 0.001 ARG 4 264 *********************** 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 951 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 705 time to evaluate : 4.583 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 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 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 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: 2 232 PHE cc_start: 0.4812 (m-80) cc_final: 0.2977 (m-80) REVERT: 2 284 LYS cc_start: 0.6302 (pptt) cc_final: 0.5936 (ttpt) REVERT: 2 340 CYS cc_start: 0.8639 (m) cc_final: 0.8237 (p) REVERT: 2 351 GLU cc_start: 0.6191 (pm20) cc_final: 0.5467 (tp30) REVERT: 2 488 GLU cc_start: 0.6677 (mm-30) cc_final: 0.5866 (mm-30) REVERT: 2 496 HIS cc_start: 0.5868 (p-80) cc_final: 0.5403 (p-80) REVERT: 2 605 LEU cc_start: 0.7235 (tp) cc_final: 0.6721 (tp) REVERT: 2 662 LYS cc_start: 0.8799 (mttt) cc_final: 0.8502 (mtmm) REVERT: 2 670 LYS cc_start: 0.5603 (pttp) cc_final: 0.4562 (mttp) REVERT: 2 744 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6952 (mm) REVERT: 2 752 GLU cc_start: 0.6044 (pt0) cc_final: 0.5477 (pt0) REVERT: 2 754 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.6169 (m170) REVERT: 3 36 MET cc_start: 0.5153 (mmp) cc_final: 0.4725 (ttm) REVERT: 3 151 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7354 (t) REVERT: 3 201 MET cc_start: 0.6178 (tpt) cc_final: 0.5937 (mmm) REVERT: 3 218 CYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8302 (t) REVERT: 3 233 GLN cc_start: 0.5089 (OUTLIER) cc_final: 0.4766 (mp10) REVERT: 3 253 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6133 (t80) REVERT: 3 286 LYS cc_start: 0.5062 (tptt) cc_final: 0.4544 (tptp) REVERT: 3 296 LYS cc_start: 0.6199 (mttt) cc_final: 0.5631 (pttt) REVERT: 3 364 THR cc_start: 0.5745 (OUTLIER) cc_final: 0.5252 (p) REVERT: 3 407 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7931 (p0) REVERT: 3 418 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.6091 (m-70) REVERT: 3 462 GLU cc_start: 0.8290 (tp30) cc_final: 0.7292 (tp30) REVERT: 3 470 LEU cc_start: 0.6266 (mp) cc_final: 0.5512 (pp) REVERT: 3 482 ASP cc_start: 0.5421 (t0) cc_final: 0.5217 (t0) REVERT: 3 562 MET cc_start: 0.6607 (tmm) cc_final: 0.6258 (ttm) REVERT: 3 563 ARG cc_start: 0.7502 (ttm170) cc_final: 0.7132 (ttp80) REVERT: 3 572 MET cc_start: 0.6527 (mmp) cc_final: 0.5039 (mmp) REVERT: 4 188 ASN cc_start: 0.6198 (m-40) cc_final: 0.5927 (p0) REVERT: 4 211 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7156 (tp) REVERT: 4 480 LYS cc_start: 0.6292 (ptpt) cc_final: 0.5535 (mmtp) REVERT: 4 513 ASP cc_start: 0.6629 (m-30) cc_final: 0.5360 (p0) REVERT: 4 524 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: 4 593 MET cc_start: 0.5586 (mtm) cc_final: 0.3570 (tmm) REVERT: 4 595 GLN cc_start: 0.7947 (mt0) cc_final: 0.7657 (mm110) REVERT: 4 661 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8708 (p0) REVERT: 4 680 GLU cc_start: 0.1342 (pm20) cc_final: 0.0257 (mt-10) REVERT: 4 695 TYR cc_start: 0.8728 (t80) cc_final: 0.8400 (t80) REVERT: 5 210 MET cc_start: 0.7701 (mmm) cc_final: 0.7179 (mmp) REVERT: 5 216 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6964 (p) REVERT: 5 239 HIS cc_start: 0.7581 (p90) cc_final: 0.7350 (p90) REVERT: 5 245 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.6209 (t0) REVERT: 5 282 VAL cc_start: 0.4854 (OUTLIER) cc_final: 0.4634 (m) REVERT: 5 360 LYS cc_start: 0.2707 (mmtt) cc_final: 0.1952 (mmtm) REVERT: 5 379 ASP cc_start: 0.7095 (t0) cc_final: 0.6617 (t0) REVERT: 5 417 LYS cc_start: 0.8002 (pttt) cc_final: 0.7017 (mptt) REVERT: 5 468 LYS cc_start: 0.7247 (mmtm) cc_final: 0.6544 (mmtp) REVERT: 5 558 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.5030 (t80) REVERT: 5 641 ARG cc_start: 0.6709 (mmt180) cc_final: 0.6277 (mmm160) REVERT: 6 55 LEU cc_start: 0.5261 (tt) cc_final: 0.4871 (pt) REVERT: 6 115 HIS cc_start: 0.7641 (m170) cc_final: 0.7309 (m170) REVERT: 6 116 LYS cc_start: 0.5965 (mmtt) cc_final: 0.5534 (ttmm) REVERT: 6 219 GLU cc_start: 0.6446 (mp0) cc_final: 0.6153 (pm20) REVERT: 6 284 LEU cc_start: 0.2900 (OUTLIER) cc_final: 0.2314 (pp) REVERT: 6 288 MET cc_start: 0.7719 (tmm) cc_final: 0.7221 (tmm) REVERT: 6 296 GLN cc_start: 0.7777 (tp-100) cc_final: 0.6782 (tt0) REVERT: 6 309 MET cc_start: 0.3392 (mtp) cc_final: 0.1494 (tmm) REVERT: 6 332 MET cc_start: 0.4121 (mpp) cc_final: 0.3166 (tpt) REVERT: 6 546 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6475 (t0) REVERT: 6 584 HIS cc_start: 0.6958 (m90) cc_final: 0.6228 (t-170) REVERT: 6 639 GLU cc_start: 0.4196 (tm-30) cc_final: 0.3436 (tm-30) REVERT: 7 83 GLU cc_start: 0.5087 (mm-30) cc_final: 0.4659 (pp20) REVERT: 7 109 MET cc_start: 0.4509 (ttm) cc_final: 0.3729 (mtp) REVERT: 7 255 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.5616 (pt) REVERT: 7 256 MET cc_start: 0.7472 (tmm) cc_final: 0.6845 (mtt) REVERT: 7 281 MET cc_start: 0.7744 (mtm) cc_final: 0.7027 (mtp) REVERT: 7 282 ARG cc_start: 0.7526 (tmt-80) cc_final: 0.6202 (ttm-80) REVERT: 7 380 MET cc_start: 0.5731 (ppp) cc_final: 0.5210 (ptt) REVERT: 7 419 MET cc_start: -0.5321 (ttp) cc_final: -0.5674 (mmt) REVERT: 7 438 ASP cc_start: 0.5326 (p0) cc_final: 0.5005 (p0) REVERT: 7 494 ARG cc_start: 0.4541 (ptm-80) cc_final: 0.3434 (ttm170) REVERT: 7 527 ARG cc_start: 0.7430 (ttp80) cc_final: 0.6327 (mmt180) REVERT: 7 568 ARG cc_start: 0.7385 (ttp80) cc_final: 0.7146 (ttp-170) REVERT: A 53 MET cc_start: 0.5718 (mpp) cc_final: 0.4740 (mtm) REVERT: A 201 MET cc_start: 0.6646 (tpp) cc_final: 0.6374 (tpt) REVERT: A 262 GLN cc_start: 0.4395 (OUTLIER) cc_final: 0.3419 (tm130) REVERT: A 507 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6135 (mt) REVERT: A 514 CYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6809 (m) REVERT: H 7 MET cc_start: 0.4494 (mtp) cc_final: 0.3463 (mmp) REVERT: H 61 ARG cc_start: 0.7034 (pmt-80) cc_final: 0.6308 (pmt-80) REVERT: H 80 CYS cc_start: 0.7454 (t) cc_final: 0.6672 (t) REVERT: L 82 LYS cc_start: 0.7441 (mmmm) cc_final: 0.7163 (mmmm) REVERT: L 93 MET cc_start: 0.6208 (mpp) cc_final: 0.4493 (tpp) REVERT: L 129 ARG cc_start: 0.7786 (tmm-80) cc_final: 0.7510 (tmm-80) REVERT: M 101 PHE cc_start: 0.4465 (t80) cc_final: 0.4229 (t80) REVERT: N 50 MET cc_start: 0.7848 (ttp) cc_final: 0.7431 (ttp) REVERT: N 157 THR cc_start: 0.6036 (OUTLIER) cc_final: 0.5782 (p) REVERT: N 172 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7170 (mp) outliers start: 246 outliers final: 138 residues processed: 892 average time/residue: 0.5322 time to fit residues: 761.8110 Evaluate side-chains 793 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 631 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 211 ASN Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 357 ASN Chi-restraints excluded: chain 2 residue 380 ASP Chi-restraints excluded: chain 2 residue 383 LEU Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 660 LEU Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 2 residue 768 VAL Chi-restraints excluded: chain 2 residue 788 MET Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 151 VAL Chi-restraints excluded: chain 3 residue 156 TYR Chi-restraints excluded: chain 3 residue 218 CYS Chi-restraints excluded: chain 3 residue 233 GLN Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 328 THR Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 386 GLN Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 524 TYR Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 647 ASP Chi-restraints excluded: chain 4 residue 661 ASP Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 5 residue 26 ASN Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 282 VAL Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 414 SER Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 502 ASP Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 85 CYS Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 193 LEU Chi-restraints excluded: chain 6 residue 194 PHE Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 335 ASP Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 410 TYR Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 163 VAL Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 255 ILE Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 421 ASP Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 514 CYS Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 158 GLU Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 172 ILE 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: 8.9990 chunk 237 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 306 optimal weight: 6.9990 chunk 458 optimal weight: 2.9990 chunk 485 optimal weight: 0.0270 chunk 239 optimal weight: 0.9980 chunk 434 optimal weight: 0.0070 chunk 130 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 210 GLN ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 658 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 656 GLN ** 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** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 461 GLN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 341 ASN 6 396 GLN 6 466 HIS 6 595 GLN 7 42 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** H 109 GLN H 120 ASN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 HIS ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41733 Z= 0.184 Angle : 0.703 12.759 56502 Z= 0.355 Chirality : 0.045 0.236 6362 Planarity : 0.005 0.066 7230 Dihedral : 11.969 152.322 6063 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.30 % Favored : 87.68 % Rotamer: Outliers : 5.26 % Allowed : 23.42 % Favored : 71.33 % 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: -3.80 (0.11), residues: 5000 helix: -1.37 (0.12), residues: 1609 sheet: -3.10 (0.19), residues: 561 loop : -3.23 (0.10), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 170 HIS 0.010 0.001 HIS H 199 PHE 0.026 0.002 PHE 7 77 TYR 0.021 0.001 TYR M 107 ARG 0.007 0.000 ARG 5 617 *********************** 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 911 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 678 time to evaluate : 4.419 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 284 LYS cc_start: 0.6333 (pptt) cc_final: 0.5911 (ttpt) REVERT: 2 351 GLU cc_start: 0.6258 (pm20) cc_final: 0.5640 (tp30) REVERT: 2 466 MET cc_start: -0.1026 (ttm) cc_final: -0.1300 (ttm) REVERT: 2 488 GLU cc_start: 0.6649 (mm-30) cc_final: 0.5811 (mm-30) REVERT: 2 496 HIS cc_start: 0.5978 (p-80) cc_final: 0.5555 (p-80) REVERT: 2 553 GLU cc_start: 0.6476 (mp0) cc_final: 0.5434 (tp30) REVERT: 2 605 LEU cc_start: 0.7172 (tp) cc_final: 0.6696 (tp) REVERT: 2 662 LYS cc_start: 0.8789 (mttt) cc_final: 0.8541 (mtmm) REVERT: 2 670 LYS cc_start: 0.5554 (pttp) cc_final: 0.4623 (mttp) REVERT: 2 752 GLU cc_start: 0.6093 (pt0) cc_final: 0.5494 (pt0) REVERT: 3 36 MET cc_start: 0.4911 (mmp) cc_final: 0.4592 (ttm) REVERT: 3 65 ASN cc_start: 0.6060 (t0) cc_final: 0.5684 (t0) REVERT: 3 85 ASP cc_start: 0.8142 (t0) cc_final: 0.7842 (t0) REVERT: 3 100 GLU cc_start: 0.7213 (mp0) cc_final: 0.6914 (mp0) REVERT: 3 151 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7629 (t) REVERT: 3 155 LYS cc_start: 0.7018 (tptp) cc_final: 0.6534 (tttt) REVERT: 3 241 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6177 (mp) REVERT: 3 253 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6095 (t80) REVERT: 3 268 GLU cc_start: 0.7527 (tp30) cc_final: 0.7254 (tp30) REVERT: 3 296 LYS cc_start: 0.6269 (mttt) cc_final: 0.5656 (pttt) REVERT: 3 348 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.4906 (tp40) REVERT: 3 364 THR cc_start: 0.5524 (OUTLIER) cc_final: 0.5068 (p) REVERT: 3 407 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8193 (p0) REVERT: 3 418 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.5542 (m-70) REVERT: 3 462 GLU cc_start: 0.8235 (tp30) cc_final: 0.7273 (tp30) REVERT: 3 470 LEU cc_start: 0.6122 (mp) cc_final: 0.5304 (pp) REVERT: 3 562 MET cc_start: 0.6774 (tmm) cc_final: 0.6560 (ttm) REVERT: 3 563 ARG cc_start: 0.7597 (ttm170) cc_final: 0.7276 (ttp80) REVERT: 4 188 ASN cc_start: 0.6719 (m-40) cc_final: 0.6437 (p0) REVERT: 4 193 GLN cc_start: 0.6686 (pp30) cc_final: 0.6463 (pp30) REVERT: 4 513 ASP cc_start: 0.6684 (m-30) cc_final: 0.5477 (p0) REVERT: 4 521 MET cc_start: 0.5932 (ppp) cc_final: 0.5717 (ppp) REVERT: 4 593 MET cc_start: 0.5138 (mtm) cc_final: 0.3202 (tmm) REVERT: 4 680 GLU cc_start: 0.1292 (pm20) cc_final: 0.0274 (mt-10) REVERT: 4 695 TYR cc_start: 0.8751 (t80) cc_final: 0.8395 (t80) REVERT: 5 99 ARG cc_start: 0.6027 (ttp-110) cc_final: 0.5762 (ttp-110) REVERT: 5 210 MET cc_start: 0.7656 (mmm) cc_final: 0.7143 (mmp) REVERT: 5 216 CYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6877 (p) REVERT: 5 220 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.4747 (tm-30) REVERT: 5 239 HIS cc_start: 0.7503 (p90) cc_final: 0.7271 (p90) REVERT: 5 245 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6418 (t0) REVERT: 5 307 ARG cc_start: 0.5458 (OUTLIER) cc_final: 0.5128 (pmt170) REVERT: 5 379 ASP cc_start: 0.7127 (t70) cc_final: 0.6659 (t0) REVERT: 5 416 MET cc_start: 0.7056 (ppp) cc_final: 0.6811 (ppp) REVERT: 5 417 LYS cc_start: 0.8033 (pttt) cc_final: 0.6913 (mptt) REVERT: 5 468 LYS cc_start: 0.7267 (mmtm) cc_final: 0.6579 (mmtp) REVERT: 5 558 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.5336 (t80) REVERT: 5 641 ARG cc_start: 0.6930 (mmt180) cc_final: 0.6479 (mmm160) REVERT: 6 55 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.4826 (pt) REVERT: 6 76 GLU cc_start: 0.6761 (tt0) cc_final: 0.6375 (tt0) REVERT: 6 219 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (pm20) REVERT: 6 284 LEU cc_start: 0.3377 (OUTLIER) cc_final: 0.2822 (pp) REVERT: 6 288 MET cc_start: 0.7786 (tmm) cc_final: 0.7332 (tmm) REVERT: 6 296 GLN cc_start: 0.7873 (tp-100) cc_final: 0.6943 (tt0) REVERT: 6 309 MET cc_start: 0.3414 (mtp) cc_final: 0.1585 (tmm) REVERT: 6 332 MET cc_start: 0.4008 (mpp) cc_final: 0.3238 (tpt) REVERT: 6 546 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6600 (t0) REVERT: 6 584 HIS cc_start: 0.7039 (m90) cc_final: 0.6325 (t-170) REVERT: 7 83 GLU cc_start: 0.4937 (mm-30) cc_final: 0.4592 (pp20) REVERT: 7 215 LYS cc_start: 0.3014 (OUTLIER) cc_final: 0.1527 (tttp) REVERT: 7 231 LYS cc_start: 0.7595 (mtpp) cc_final: 0.7371 (mtpp) REVERT: 7 256 MET cc_start: 0.7260 (tmm) cc_final: 0.6809 (mtt) REVERT: 7 264 MET cc_start: 0.8196 (mtt) cc_final: 0.7957 (mtt) REVERT: 7 281 MET cc_start: 0.7737 (mtm) cc_final: 0.7009 (mtp) REVERT: 7 282 ARG cc_start: 0.7602 (tmt-80) cc_final: 0.6329 (ttm-80) REVERT: 7 343 GLU cc_start: 0.5095 (mm-30) cc_final: 0.4866 (mm-30) REVERT: 7 380 MET cc_start: 0.5891 (ppp) cc_final: 0.5287 (ptt) REVERT: 7 494 ARG cc_start: 0.4645 (ptm-80) cc_final: 0.3522 (ptp-170) REVERT: 7 514 ARG cc_start: 0.7375 (ttm110) cc_final: 0.6700 (tpt170) REVERT: 7 527 ARG cc_start: 0.7441 (ttp80) cc_final: 0.6337 (mmt180) REVERT: 7 568 ARG cc_start: 0.7500 (ttp80) cc_final: 0.7207 (ttp-170) REVERT: A 53 MET cc_start: 0.5752 (mpp) cc_final: 0.4747 (mtm) REVERT: A 201 MET cc_start: 0.6580 (tpp) cc_final: 0.6277 (tpt) REVERT: A 230 MET cc_start: 0.6643 (mtm) cc_final: 0.6292 (mtt) REVERT: A 507 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6070 (mp) REVERT: H 7 MET cc_start: 0.4732 (mtp) cc_final: 0.3212 (mmp) REVERT: H 80 CYS cc_start: 0.7426 (t) cc_final: 0.6441 (t) REVERT: L 93 MET cc_start: 0.5498 (mpp) cc_final: 0.4084 (tpp) REVERT: L 120 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7921 (mm) REVERT: L 129 ARG cc_start: 0.7544 (tmm-80) cc_final: 0.7277 (tmm-80) REVERT: L 151 LEU cc_start: 0.6987 (mp) cc_final: 0.6540 (mt) REVERT: M 101 PHE cc_start: 0.4888 (t80) cc_final: 0.4309 (t80) REVERT: N 50 MET cc_start: 0.7745 (ttp) cc_final: 0.7392 (ttp) REVERT: N 157 THR cc_start: 0.6149 (OUTLIER) cc_final: 0.5828 (p) REVERT: N 172 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7235 (mp) outliers start: 233 outliers final: 144 residues processed: 849 average time/residue: 0.5298 time to fit residues: 725.0302 Evaluate side-chains 784 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 620 time to evaluate : 4.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 357 ASN Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 506 ILE Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 2 residue 788 MET Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 151 VAL Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 476 LEU Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 230 ILE Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 386 GLN Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 427 VAL Chi-restraints excluded: chain 4 residue 477 ASP Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 528 LEU Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 647 ASP Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 296 THR Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 402 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 85 CYS Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 132 SER Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 335 ASP Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 421 ASP Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 158 GLU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 172 ILE Chi-restraints excluded: chain N residue 193 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 404 optimal weight: 0.6980 chunk 275 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 361 optimal weight: 0.7980 chunk 200 optimal weight: 0.0970 chunk 414 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 435 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 79 HIS ** 6 134 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** ** 7 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN ** 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: 0.5724 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 41733 Z= 0.182 Angle : 0.687 12.308 56502 Z= 0.345 Chirality : 0.044 0.184 6362 Planarity : 0.005 0.064 7230 Dihedral : 11.668 158.427 6051 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.30 % Favored : 87.68 % Rotamer: Outliers : 5.37 % Allowed : 24.32 % Favored : 70.31 % 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: -1.14 (0.13), residues: 1601 sheet: -2.87 (0.20), residues: 528 loop : -3.09 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 170 HIS 0.012 0.001 HIS 6 79 PHE 0.025 0.002 PHE 7 77 TYR 0.026 0.001 TYR 7 182 ARG 0.006 0.000 ARG 7 225 *********************** 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 896 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 658 time to evaluate : 4.390 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 212 MET cc_start: 0.6522 (mmt) cc_final: 0.5514 (mtp) REVERT: 2 284 LYS cc_start: 0.6284 (pptt) cc_final: 0.5877 (ttpt) REVERT: 2 351 GLU cc_start: 0.6372 (pm20) cc_final: 0.5666 (tp30) REVERT: 2 389 ASP cc_start: 0.7060 (t0) cc_final: 0.6728 (t0) REVERT: 2 466 MET cc_start: -0.1137 (ttm) cc_final: -0.1471 (ttm) REVERT: 2 488 GLU cc_start: 0.6586 (mm-30) cc_final: 0.5821 (mm-30) REVERT: 2 496 HIS cc_start: 0.6110 (p-80) cc_final: 0.5659 (p-80) REVERT: 2 553 GLU cc_start: 0.6653 (mp0) cc_final: 0.5445 (tp30) REVERT: 2 587 GLU cc_start: 0.4135 (OUTLIER) cc_final: 0.3859 (tm-30) REVERT: 2 605 LEU cc_start: 0.7206 (tp) cc_final: 0.6776 (tp) REVERT: 2 662 LYS cc_start: 0.8782 (mttt) cc_final: 0.8538 (mtmm) REVERT: 2 670 LYS cc_start: 0.5556 (pttp) cc_final: 0.4706 (mttp) REVERT: 2 693 PRO cc_start: 0.3682 (Cg_endo) cc_final: 0.3259 (Cg_exo) REVERT: 2 715 ILE cc_start: 0.5184 (OUTLIER) cc_final: 0.4651 (mm) REVERT: 2 727 LEU cc_start: 0.2087 (tt) cc_final: 0.1802 (mp) REVERT: 2 752 GLU cc_start: 0.6095 (pt0) cc_final: 0.5503 (pt0) REVERT: 3 65 ASN cc_start: 0.6193 (t0) cc_final: 0.5776 (t0) REVERT: 3 85 ASP cc_start: 0.8338 (t0) cc_final: 0.8082 (t0) REVERT: 3 100 GLU cc_start: 0.7256 (mp0) cc_final: 0.6807 (mp0) REVERT: 3 140 ARG cc_start: 0.7181 (ptt180) cc_final: 0.6710 (ptt180) REVERT: 3 155 LYS cc_start: 0.7104 (tptp) cc_final: 0.6639 (tttt) REVERT: 3 201 MET cc_start: 0.6699 (mmm) cc_final: 0.6180 (mpp) REVERT: 3 218 CYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8307 (t) REVERT: 3 241 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6268 (mp) REVERT: 3 253 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5962 (t80) REVERT: 3 268 GLU cc_start: 0.7413 (tp30) cc_final: 0.7200 (tp30) REVERT: 3 296 LYS cc_start: 0.6275 (mttt) cc_final: 0.5653 (pttt) REVERT: 3 348 GLN cc_start: 0.5672 (OUTLIER) cc_final: 0.4310 (tp40) REVERT: 3 364 THR cc_start: 0.5487 (OUTLIER) cc_final: 0.5084 (p) REVERT: 3 401 VAL cc_start: 0.5738 (t) cc_final: 0.5527 (t) REVERT: 3 407 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8130 (p0) REVERT: 3 418 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5848 (m-70) REVERT: 3 462 GLU cc_start: 0.8218 (tp30) cc_final: 0.7936 (tp30) REVERT: 3 470 LEU cc_start: 0.6064 (mp) cc_final: 0.5383 (pp) REVERT: 3 563 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7501 (ttp80) REVERT: 4 513 ASP cc_start: 0.6773 (m-30) cc_final: 0.5615 (p0) REVERT: 4 521 MET cc_start: 0.6218 (ppp) cc_final: 0.5980 (ppp) REVERT: 4 630 LYS cc_start: 0.7731 (tttm) cc_final: 0.7469 (mmmt) REVERT: 4 680 GLU cc_start: 0.1320 (OUTLIER) cc_final: 0.0308 (mt-10) REVERT: 4 695 TYR cc_start: 0.8737 (t80) cc_final: 0.8349 (t80) REVERT: 5 210 MET cc_start: 0.7711 (mmm) cc_final: 0.7179 (mmp) REVERT: 5 216 CYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6945 (p) REVERT: 5 220 GLN cc_start: 0.6240 (OUTLIER) cc_final: 0.4863 (tt0) REVERT: 5 239 HIS cc_start: 0.7463 (p90) cc_final: 0.7221 (p90) REVERT: 5 245 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6289 (t0) REVERT: 5 307 ARG cc_start: 0.5570 (OUTLIER) cc_final: 0.5203 (pmt170) REVERT: 5 379 ASP cc_start: 0.7116 (t70) cc_final: 0.6629 (t0) REVERT: 5 417 LYS cc_start: 0.8057 (pttt) cc_final: 0.6952 (mptt) REVERT: 5 468 LYS cc_start: 0.7359 (mmtm) cc_final: 0.6595 (mmmt) REVERT: 5 558 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.4850 (t80) REVERT: 5 562 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7696 (mp) REVERT: 5 641 ARG cc_start: 0.6962 (mmt180) cc_final: 0.6392 (mmm160) REVERT: 6 55 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.4997 (pt) REVERT: 6 284 LEU cc_start: 0.3450 (OUTLIER) cc_final: 0.2824 (pp) REVERT: 6 288 MET cc_start: 0.7788 (tmm) cc_final: 0.7358 (tmm) REVERT: 6 296 GLN cc_start: 0.7781 (tp-100) cc_final: 0.6810 (tt0) REVERT: 6 309 MET cc_start: 0.3382 (mtp) cc_final: 0.1828 (tmm) REVERT: 6 332 MET cc_start: 0.3972 (mpp) cc_final: 0.3321 (tpt) REVERT: 6 546 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6517 (t0) REVERT: 6 584 HIS cc_start: 0.7219 (m90) cc_final: 0.6443 (t-170) REVERT: 7 83 GLU cc_start: 0.4952 (mm-30) cc_final: 0.4510 (pp20) REVERT: 7 215 LYS cc_start: 0.2903 (OUTLIER) cc_final: 0.1466 (tttp) REVERT: 7 255 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5643 (pt) REVERT: 7 256 MET cc_start: 0.7096 (tmm) cc_final: 0.6681 (mtt) REVERT: 7 264 MET cc_start: 0.8144 (mtt) cc_final: 0.7841 (mtt) REVERT: 7 281 MET cc_start: 0.7787 (mtm) cc_final: 0.7051 (mtp) REVERT: 7 343 GLU cc_start: 0.5114 (mm-30) cc_final: 0.4904 (mm-30) REVERT: 7 380 MET cc_start: 0.5913 (ppp) cc_final: 0.5501 (ptt) REVERT: 7 494 ARG cc_start: 0.4739 (ptm-80) cc_final: 0.3786 (ttm170) REVERT: 7 514 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6657 (tpt170) REVERT: 7 527 ARG cc_start: 0.7512 (ttp80) cc_final: 0.6397 (mmt180) REVERT: 7 568 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7250 (ttp-170) REVERT: A 53 MET cc_start: 0.5838 (mpp) cc_final: 0.4728 (mtm) REVERT: A 130 PHE cc_start: 0.6397 (t80) cc_final: 0.6053 (t80) REVERT: A 201 MET cc_start: 0.6551 (tpp) cc_final: 0.6223 (tpt) REVERT: A 314 LYS cc_start: 0.5951 (mttm) cc_final: 0.5678 (mttp) REVERT: A 507 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6133 (mp) REVERT: H 80 CYS cc_start: 0.7513 (t) cc_final: 0.6555 (t) REVERT: H 115 GLU cc_start: 0.4989 (OUTLIER) cc_final: 0.3900 (mt-10) REVERT: L 18 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7371 (mt) REVERT: L 93 MET cc_start: 0.5767 (mpp) cc_final: 0.4369 (tpp) REVERT: M 101 PHE cc_start: 0.4784 (t80) cc_final: 0.4163 (t80) REVERT: N 50 MET cc_start: 0.7579 (ttp) cc_final: 0.7317 (ttp) REVERT: N 157 THR cc_start: 0.6179 (OUTLIER) cc_final: 0.5833 (p) REVERT: N 172 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7241 (mp) outliers start: 238 outliers final: 157 residues processed: 838 average time/residue: 0.5491 time to fit residues: 742.2234 Evaluate side-chains 783 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 600 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 178 THR Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 211 ASN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 357 ASN Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 380 ASP Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 587 GLU Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 715 ILE Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 2 residue 788 MET Chi-restraints excluded: chain 3 residue 11 ASP Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 55 ASN Chi-restraints excluded: chain 3 residue 60 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 218 CYS Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 298 LEU Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 640 ILE Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 386 GLN Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 477 ASP Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 647 ASP Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 26 ASN Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 100 GLU Chi-restraints excluded: chain 5 residue 117 HIS Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 297 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 335 ASP Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 546 ASP Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 568 VAL Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 255 ILE Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 355 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 385 VAL Chi-restraints excluded: chain 7 residue 421 ASP Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 15 ASP Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 172 ILE Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 163 optimal weight: 0.0060 chunk 436 optimal weight: 0.5980 chunk 95 optimal weight: 0.0470 chunk 284 optimal weight: 0.0170 chunk 119 optimal weight: 6.9990 chunk 485 optimal weight: 2.9990 chunk 403 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 436 GLN 2 586 HIS 2 783 GLN 3 348 GLN 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 256 ASN ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 79 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 496 ASN 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** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 ASN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41733 Z= 0.166 Angle : 0.673 11.304 56502 Z= 0.336 Chirality : 0.043 0.182 6362 Planarity : 0.005 0.065 7230 Dihedral : 11.414 163.511 6045 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.30 % Favored : 88.68 % Rotamer: Outliers : 4.74 % Allowed : 25.54 % Favored : 69.73 % 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: -3.37 (0.11), residues: 5000 helix: -0.97 (0.13), residues: 1612 sheet: -2.61 (0.20), residues: 523 loop : -3.06 (0.10), residues: 2865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 170 HIS 0.014 0.001 HIS 6 79 PHE 0.036 0.001 PHE 6 347 TYR 0.019 0.001 TYR 4 716 ARG 0.011 0.000 ARG 4 264 *********************** 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 878 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 668 time to evaluate : 4.844 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 212 MET cc_start: 0.6470 (mmt) cc_final: 0.5585 (mtp) REVERT: 2 350 MET cc_start: 0.3950 (mtt) cc_final: 0.2982 (mmt) REVERT: 2 351 GLU cc_start: 0.6281 (pm20) cc_final: 0.5664 (tp30) REVERT: 2 389 ASP cc_start: 0.6875 (t0) cc_final: 0.6555 (t0) REVERT: 2 488 GLU cc_start: 0.6584 (mm-30) cc_final: 0.5855 (mm-30) REVERT: 2 496 HIS cc_start: 0.6148 (p-80) cc_final: 0.5898 (p-80) REVERT: 2 553 GLU cc_start: 0.6534 (mp0) cc_final: 0.5177 (tp30) REVERT: 2 626 MET cc_start: -0.0547 (tmm) cc_final: -0.1840 (mpp) REVERT: 2 662 LYS cc_start: 0.8723 (mttt) cc_final: 0.8514 (mtmm) REVERT: 2 670 LYS cc_start: 0.5971 (pttp) cc_final: 0.4938 (mttp) REVERT: 2 693 PRO cc_start: 0.3735 (Cg_endo) cc_final: 0.3307 (Cg_exo) REVERT: 2 715 ILE cc_start: 0.5176 (OUTLIER) cc_final: 0.4719 (mm) REVERT: 2 752 GLU cc_start: 0.6004 (pt0) cc_final: 0.5358 (pt0) REVERT: 3 100 GLU cc_start: 0.7064 (mp0) cc_final: 0.6825 (mp0) REVERT: 3 140 ARG cc_start: 0.7173 (ptt180) cc_final: 0.6686 (ptt180) REVERT: 3 151 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7664 (t) REVERT: 3 155 LYS cc_start: 0.7066 (tptp) cc_final: 0.6597 (tttt) REVERT: 3 201 MET cc_start: 0.6600 (mmm) cc_final: 0.6114 (mpp) REVERT: 3 218 CYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8279 (t) REVERT: 3 241 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6225 (mp) REVERT: 3 253 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5823 (t80) REVERT: 3 268 GLU cc_start: 0.7781 (tp30) cc_final: 0.7431 (tp30) REVERT: 3 296 LYS cc_start: 0.6189 (mttt) cc_final: 0.5564 (pttt) REVERT: 3 314 CYS cc_start: 0.7786 (m) cc_final: 0.7524 (m) REVERT: 3 348 GLN cc_start: 0.5504 (OUTLIER) cc_final: 0.4202 (tp40) REVERT: 3 364 THR cc_start: 0.5226 (OUTLIER) cc_final: 0.4864 (p) REVERT: 3 407 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8152 (p0) REVERT: 3 418 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5846 (m-70) REVERT: 3 425 ARG cc_start: 0.2279 (mtm-85) cc_final: 0.1885 (ttm-80) REVERT: 3 462 GLU cc_start: 0.8260 (tp30) cc_final: 0.7730 (tp30) REVERT: 3 470 LEU cc_start: 0.6093 (mp) cc_final: 0.5440 (pp) REVERT: 3 562 MET cc_start: 0.7260 (ttm) cc_final: 0.6893 (tmm) REVERT: 4 480 LYS cc_start: 0.6671 (ptpt) cc_final: 0.5897 (mppt) REVERT: 4 513 ASP cc_start: 0.6762 (m-30) cc_final: 0.5629 (p0) REVERT: 4 521 MET cc_start: 0.6200 (ppp) cc_final: 0.5960 (ppp) REVERT: 4 595 GLN cc_start: 0.7870 (mt0) cc_final: 0.7262 (mt0) REVERT: 4 630 LYS cc_start: 0.7689 (tttm) cc_final: 0.7449 (mmmt) REVERT: 4 680 GLU cc_start: 0.1198 (OUTLIER) cc_final: 0.0243 (mt-10) REVERT: 4 695 TYR cc_start: 0.8650 (t80) cc_final: 0.8281 (t80) REVERT: 5 69 MET cc_start: 0.6428 (mmm) cc_final: 0.6017 (mmm) REVERT: 5 138 ASP cc_start: 0.7599 (p0) cc_final: 0.7386 (p0) REVERT: 5 210 MET cc_start: 0.7666 (mmm) cc_final: 0.7159 (mmp) REVERT: 5 216 CYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6689 (p) REVERT: 5 220 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.4769 (tt0) REVERT: 5 245 ASP cc_start: 0.6453 (OUTLIER) cc_final: 0.6079 (t0) REVERT: 5 307 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.5316 (pmt170) REVERT: 5 379 ASP cc_start: 0.7227 (t70) cc_final: 0.6725 (t0) REVERT: 5 417 LYS cc_start: 0.7999 (pttt) cc_final: 0.7078 (mptt) REVERT: 5 468 LYS cc_start: 0.7376 (mmtm) cc_final: 0.6626 (mmtp) REVERT: 5 558 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.5100 (t80) REVERT: 5 562 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7627 (mp) REVERT: 5 641 ARG cc_start: 0.6989 (mmt180) cc_final: 0.6471 (mmm160) REVERT: 6 55 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.4942 (pt) REVERT: 6 284 LEU cc_start: 0.3518 (OUTLIER) cc_final: 0.2935 (pp) REVERT: 6 296 GLN cc_start: 0.7745 (tp-100) cc_final: 0.6723 (tt0) REVERT: 6 309 MET cc_start: 0.4423 (mtp) cc_final: 0.3492 (ptm) REVERT: 6 332 MET cc_start: 0.3576 (mpp) cc_final: 0.3070 (tpt) REVERT: 6 442 MET cc_start: 0.7212 (mmm) cc_final: 0.6894 (mmm) REVERT: 6 584 HIS cc_start: 0.6995 (m90) cc_final: 0.6420 (t-170) REVERT: 6 623 MET cc_start: 0.4660 (mtp) cc_final: 0.4399 (mtp) REVERT: 7 83 GLU cc_start: 0.4853 (mm-30) cc_final: 0.4483 (pp20) REVERT: 7 93 VAL cc_start: 0.3896 (OUTLIER) cc_final: 0.3457 (p) REVERT: 7 215 LYS cc_start: 0.3268 (OUTLIER) cc_final: 0.1727 (tttp) REVERT: 7 223 GLN cc_start: 0.8355 (tp-100) cc_final: 0.7843 (tp-100) REVERT: 7 248 HIS cc_start: 0.7227 (t-90) cc_final: 0.6960 (t-90) REVERT: 7 253 MET cc_start: 0.6781 (ptt) cc_final: 0.6532 (ptm) REVERT: 7 255 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5693 (pt) REVERT: 7 256 MET cc_start: 0.7012 (tmm) cc_final: 0.6548 (mtt) REVERT: 7 264 MET cc_start: 0.8119 (mtt) cc_final: 0.7827 (mtt) REVERT: 7 281 MET cc_start: 0.7807 (mtm) cc_final: 0.7076 (mtp) REVERT: 7 380 MET cc_start: 0.5373 (ppp) cc_final: 0.5134 (ptt) REVERT: 7 391 LEU cc_start: 0.8539 (tp) cc_final: 0.8260 (pp) REVERT: 7 494 ARG cc_start: 0.4869 (ptm-80) cc_final: 0.3898 (ttm170) REVERT: 7 527 ARG cc_start: 0.7487 (ttp80) cc_final: 0.6415 (mmt180) REVERT: 7 568 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7336 (ttp-170) REVERT: A 53 MET cc_start: 0.5858 (mpp) cc_final: 0.4751 (mtm) REVERT: A 201 MET cc_start: 0.6372 (tpp) cc_final: 0.6053 (tpt) REVERT: A 314 LYS cc_start: 0.6085 (mttm) cc_final: 0.5832 (mttp) REVERT: A 507 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6085 (mp) REVERT: H 7 MET cc_start: 0.4531 (mtp) cc_final: 0.4022 (mtp) REVERT: H 61 ARG cc_start: 0.7140 (pmt-80) cc_final: 0.6167 (ptm-80) REVERT: H 130 MET cc_start: 0.6243 (mmm) cc_final: 0.5280 (tpp) REVERT: L 18 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7476 (mt) REVERT: L 93 MET cc_start: 0.5367 (mpp) cc_final: 0.4438 (tpp) REVERT: M 32 GLN cc_start: 0.8503 (mt0) cc_final: 0.7808 (mm-40) REVERT: M 33 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7039 (mpp80) REVERT: M 101 PHE cc_start: 0.4892 (t80) cc_final: 0.4281 (t80) REVERT: M 173 MET cc_start: 0.6936 (pmm) cc_final: 0.6428 (pmm) REVERT: N 157 THR cc_start: 0.6103 (OUTLIER) cc_final: 0.5898 (p) REVERT: N 172 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7114 (mp) outliers start: 210 outliers final: 138 residues processed: 826 average time/residue: 0.5542 time to fit residues: 737.3743 Evaluate side-chains 775 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 612 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 178 THR Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 357 ASN Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 415 GLN Chi-restraints excluded: chain 2 residue 436 GLN Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 454 LYS Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 715 ILE Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 2 residue 788 MET Chi-restraints excluded: chain 3 residue 11 ASP Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 127 ILE Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 151 VAL Chi-restraints excluded: chain 3 residue 218 CYS Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 418 HIS Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 386 GLN Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 477 ASP Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 220 GLN Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 127 THR Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 255 ILE Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 327 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 172 ILE Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 193 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 468 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 354 optimal weight: 0.2980 chunk 274 optimal weight: 9.9990 chunk 408 optimal weight: 2.9990 chunk 271 optimal weight: 9.9990 chunk 483 optimal weight: 0.0060 chunk 302 optimal weight: 2.9990 chunk 294 optimal weight: 0.2980 chunk 223 optimal weight: 0.0170 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 586 HIS ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN 3 567 HIS ** 3 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 533 GLN ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 26 ASN ** 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** 6 115 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 612 GLN 7 266 GLN ** 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 529 ASN H 51 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 HIS L 166 HIS ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 ASN N 59 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41733 Z= 0.165 Angle : 0.665 11.452 56502 Z= 0.330 Chirality : 0.043 0.219 6362 Planarity : 0.005 0.073 7230 Dihedral : 11.179 158.339 6034 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.22 % Favored : 88.76 % Rotamer: Outliers : 4.80 % Allowed : 25.67 % Favored : 69.52 % 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: -3.22 (0.11), residues: 5000 helix: -0.84 (0.13), residues: 1611 sheet: -2.51 (0.20), residues: 534 loop : -2.98 (0.11), residues: 2855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 170 HIS 0.012 0.001 HIS 6 115 PHE 0.025 0.001 PHE 7 77 TYR 0.020 0.001 TYR L 92 ARG 0.022 0.000 ARG 4 531 *********************** 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 853 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 640 time to evaluate : 4.622 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 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 REVERT: 2 212 MET cc_start: 0.6460 (mmt) cc_final: 0.5620 (mtp) REVERT: 2 350 MET cc_start: 0.3989 (mtt) cc_final: 0.3028 (mmt) REVERT: 2 351 GLU cc_start: 0.6171 (pm20) cc_final: 0.5671 (tp30) REVERT: 2 488 GLU cc_start: 0.6520 (mm-30) cc_final: 0.5776 (mm-30) REVERT: 2 496 HIS cc_start: 0.6122 (p-80) cc_final: 0.5801 (p-80) REVERT: 2 553 GLU cc_start: 0.6634 (mp0) cc_final: 0.5210 (tp30) REVERT: 2 670 LYS cc_start: 0.5681 (pttp) cc_final: 0.4804 (mttp) REVERT: 2 693 PRO cc_start: 0.3882 (Cg_endo) cc_final: 0.3495 (Cg_exo) REVERT: 2 752 GLU cc_start: 0.5913 (pt0) cc_final: 0.5292 (pt0) REVERT: 3 88 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.5853 (t80) REVERT: 3 140 ARG cc_start: 0.7022 (ptt180) cc_final: 0.6751 (ptt180) REVERT: 3 155 LYS cc_start: 0.7076 (tptp) cc_final: 0.6620 (tttt) REVERT: 3 218 CYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8306 (t) REVERT: 3 241 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6299 (mp) REVERT: 3 253 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.5903 (t80) REVERT: 3 268 GLU cc_start: 0.7726 (tp30) cc_final: 0.7423 (tp30) REVERT: 3 284 LEU cc_start: 0.7073 (pp) cc_final: 0.6539 (tp) REVERT: 3 296 LYS cc_start: 0.6167 (mttt) cc_final: 0.5580 (pttt) REVERT: 3 348 GLN cc_start: 0.5229 (OUTLIER) cc_final: 0.3932 (tp40) REVERT: 3 364 THR cc_start: 0.5134 (OUTLIER) cc_final: 0.4771 (p) REVERT: 3 407 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8165 (p0) REVERT: 3 462 GLU cc_start: 0.8210 (tp30) cc_final: 0.7705 (tp30) REVERT: 3 499 MET cc_start: 0.2130 (mmm) cc_final: 0.1619 (tmm) REVERT: 4 513 ASP cc_start: 0.6903 (m-30) cc_final: 0.5735 (p0) REVERT: 4 521 MET cc_start: 0.6337 (ppp) cc_final: 0.5955 (ppp) REVERT: 4 595 GLN cc_start: 0.7855 (mt0) cc_final: 0.7239 (mt0) REVERT: 4 630 LYS cc_start: 0.7664 (tttm) cc_final: 0.7437 (mmmt) REVERT: 4 680 GLU cc_start: 0.1320 (OUTLIER) cc_final: 0.0306 (mt-10) REVERT: 4 695 TYR cc_start: 0.8670 (t80) cc_final: 0.8272 (t80) REVERT: 5 69 MET cc_start: 0.6358 (mmm) cc_final: 0.5866 (mmm) REVERT: 5 210 MET cc_start: 0.7638 (mmm) cc_final: 0.7153 (mmp) REVERT: 5 216 CYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6555 (p) REVERT: 5 226 GLU cc_start: 0.5659 (tm-30) cc_final: 0.5048 (tm-30) REVERT: 5 245 ASP cc_start: 0.6369 (OUTLIER) cc_final: 0.5964 (t0) REVERT: 5 360 LYS cc_start: 0.2079 (mmtt) cc_final: 0.1601 (mmtp) REVERT: 5 379 ASP cc_start: 0.7206 (t70) cc_final: 0.6824 (t0) REVERT: 5 417 LYS cc_start: 0.7930 (pttt) cc_final: 0.6923 (mptt) REVERT: 5 468 LYS cc_start: 0.7408 (mmtm) cc_final: 0.6724 (mmtp) REVERT: 5 558 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.5030 (t80) REVERT: 5 562 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7671 (mp) REVERT: 5 588 MET cc_start: 0.6268 (tpp) cc_final: 0.5660 (ttm) REVERT: 5 641 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6534 (mmm160) REVERT: 6 55 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5132 (pt) REVERT: 6 139 HIS cc_start: 0.6249 (m-70) cc_final: 0.6034 (m170) REVERT: 6 284 LEU cc_start: 0.3573 (OUTLIER) cc_final: 0.2965 (pp) REVERT: 6 296 GLN cc_start: 0.7628 (tp-100) cc_final: 0.6568 (tt0) REVERT: 6 309 MET cc_start: 0.4059 (mtp) cc_final: 0.2908 (ptm) REVERT: 6 332 MET cc_start: 0.3542 (mpp) cc_final: 0.3050 (tpt) REVERT: 6 442 MET cc_start: 0.7138 (mmm) cc_final: 0.6866 (mmm) REVERT: 6 584 HIS cc_start: 0.7007 (m90) cc_final: 0.6660 (t-170) REVERT: 6 623 MET cc_start: 0.4833 (mtp) cc_final: 0.4599 (mtp) REVERT: 7 83 GLU cc_start: 0.4856 (mm-30) cc_final: 0.3889 (tp30) REVERT: 7 93 VAL cc_start: 0.3624 (OUTLIER) cc_final: 0.3106 (p) REVERT: 7 215 LYS cc_start: 0.3686 (OUTLIER) cc_final: 0.2095 (tttp) REVERT: 7 223 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7878 (tp-100) REVERT: 7 248 HIS cc_start: 0.7457 (t-90) cc_final: 0.7004 (t-90) REVERT: 7 253 MET cc_start: 0.6826 (ptt) cc_final: 0.6595 (ptm) REVERT: 7 255 ILE cc_start: 0.6264 (OUTLIER) cc_final: 0.5702 (pt) REVERT: 7 256 MET cc_start: 0.6963 (tmm) cc_final: 0.6463 (mtt) REVERT: 7 266 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.5088 (mm-40) REVERT: 7 281 MET cc_start: 0.7828 (mtm) cc_final: 0.7077 (mtp) REVERT: 7 391 LEU cc_start: 0.8672 (tp) cc_final: 0.8115 (pp) REVERT: 7 400 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5364 (mtp-110) REVERT: 7 494 ARG cc_start: 0.4936 (ptm-80) cc_final: 0.4007 (ttm170) REVERT: 7 527 ARG cc_start: 0.7461 (ttp80) cc_final: 0.6411 (mmt180) REVERT: 7 568 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7361 (ttp-170) REVERT: A 53 MET cc_start: 0.6229 (mpp) cc_final: 0.5180 (mtp) REVERT: A 201 MET cc_start: 0.6206 (tpp) cc_final: 0.5815 (tpt) REVERT: A 314 LYS cc_start: 0.6111 (mttm) cc_final: 0.5903 (mttp) REVERT: A 507 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6070 (mp) REVERT: H 61 ARG cc_start: 0.7167 (pmt-80) cc_final: 0.6433 (ptm-80) REVERT: H 130 MET cc_start: 0.6011 (mmm) cc_final: 0.5259 (tpp) REVERT: L 18 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7471 (mt) REVERT: L 93 MET cc_start: 0.5229 (mpp) cc_final: 0.4469 (tpp) REVERT: L 120 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7649 (mm) REVERT: M 32 GLN cc_start: 0.8579 (mt0) cc_final: 0.7897 (mm-40) REVERT: M 33 ARG cc_start: 0.7529 (mtt180) cc_final: 0.6993 (mpp80) REVERT: M 81 HIS cc_start: 0.3442 (OUTLIER) cc_final: 0.2956 (t70) REVERT: M 101 PHE cc_start: 0.4660 (t80) cc_final: 0.4159 (t80) REVERT: M 173 MET cc_start: 0.7280 (pmm) cc_final: 0.6788 (pmm) REVERT: N 101 MET cc_start: 0.7604 (tmm) cc_final: 0.7356 (tmm) REVERT: N 120 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6732 (mp) REVERT: N 124 GLU cc_start: 0.6053 (mp0) cc_final: 0.5823 (mp0) REVERT: N 172 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7030 (mp) outliers start: 213 outliers final: 134 residues processed: 794 average time/residue: 0.5315 time to fit residues: 684.3496 Evaluate side-chains 765 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 606 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 178 THR Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 239 GLN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 357 ASN Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 3 residue 11 ASP Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 77 LEU Chi-restraints excluded: chain 3 residue 88 TYR Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 218 CYS Chi-restraints excluded: chain 3 residue 241 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 312 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 464 ILE Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 337 ASN Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 386 GLN Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 477 ASP Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 466 ILE Chi-restraints excluded: chain 5 residue 481 VAL Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 636 VAL Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 115 HIS Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 326 TRP Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 7 residue 42 HIS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 255 ILE Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 266 GLN Chi-restraints excluded: chain 7 residue 312 ILE Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 400 ARG Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain L residue 166 HIS Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 120 LEU Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 172 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 299 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 288 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 329 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 380 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 586 HIS 2 658 GLN ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 672 HIS 2 758 HIS 3 143 HIS ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 26 ASN ** 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** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 231 GLN ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 GLN 7 266 GLN ** 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** H 71 HIS ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 ASN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41733 Z= 0.224 Angle : 0.717 12.282 56502 Z= 0.361 Chirality : 0.045 0.190 6362 Planarity : 0.005 0.067 7230 Dihedral : 11.244 148.527 6025 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.58 % Favored : 87.38 % Rotamer: Outliers : 5.10 % Allowed : 25.76 % Favored : 69.14 % 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: -3.24 (0.11), residues: 5000 helix: -0.83 (0.13), residues: 1615 sheet: -2.54 (0.20), residues: 547 loop : -3.00 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 170 HIS 0.023 0.001 HIS L 166 PHE 0.042 0.002 PHE 6 347 TYR 0.032 0.002 TYR 7 182 ARG 0.010 0.001 ARG 6 542 *********************** 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 872 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 646 time to evaluate : 4.670 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 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: 2 351 GLU cc_start: 0.6147 (pm20) cc_final: 0.5655 (tp30) REVERT: 2 488 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6202 (mm-30) REVERT: 2 497 LYS cc_start: 0.5122 (OUTLIER) cc_final: 0.4849 (mptt) REVERT: 2 553 GLU cc_start: 0.6933 (mp0) cc_final: 0.5373 (tp30) REVERT: 2 554 TRP cc_start: 0.3277 (t-100) cc_final: 0.2923 (m-10) REVERT: 2 605 LEU cc_start: 0.7332 (tp) cc_final: 0.6898 (tp) REVERT: 2 670 LYS cc_start: 0.6120 (pttp) cc_final: 0.5148 (mttp) REVERT: 2 693 PRO cc_start: 0.4271 (Cg_endo) cc_final: 0.3966 (Cg_exo) REVERT: 2 752 GLU cc_start: 0.5957 (pt0) cc_final: 0.5481 (pt0) REVERT: 2 757 MET cc_start: 0.5245 (mtp) cc_final: 0.5037 (mtp) REVERT: 3 36 MET cc_start: 0.4600 (ptm) cc_final: 0.4229 (mpp) REVERT: 3 140 ARG cc_start: 0.7192 (ptt180) cc_final: 0.6949 (ptt180) REVERT: 3 155 LYS cc_start: 0.6957 (tptp) cc_final: 0.6544 (tttt) REVERT: 3 225 ARG cc_start: 0.6077 (ttm110) cc_final: 0.5664 (ttm110) REVERT: 3 253 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6178 (t80) REVERT: 3 268 GLU cc_start: 0.7983 (tp30) cc_final: 0.7673 (tp30) REVERT: 3 296 LYS cc_start: 0.6208 (mttt) cc_final: 0.5635 (pttt) REVERT: 3 348 GLN cc_start: 0.5423 (OUTLIER) cc_final: 0.3972 (tp40) REVERT: 3 364 THR cc_start: 0.5385 (OUTLIER) cc_final: 0.5093 (p) REVERT: 3 407 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8236 (p0) REVERT: 3 462 GLU cc_start: 0.8310 (tp30) cc_final: 0.7798 (tp30) REVERT: 4 513 ASP cc_start: 0.6861 (m-30) cc_final: 0.5829 (p0) REVERT: 4 521 MET cc_start: 0.6400 (ppp) cc_final: 0.5966 (ppp) REVERT: 4 595 GLN cc_start: 0.7817 (mt0) cc_final: 0.7272 (mt0) REVERT: 4 676 ARG cc_start: 0.3401 (pmt-80) cc_final: 0.1775 (ptt90) REVERT: 4 680 GLU cc_start: 0.1635 (pm20) cc_final: 0.0685 (mt-10) REVERT: 4 695 TYR cc_start: 0.8590 (t80) cc_final: 0.8251 (t80) REVERT: 5 210 MET cc_start: 0.7701 (mmm) cc_final: 0.7039 (mmp) REVERT: 5 216 CYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7027 (p) REVERT: 5 245 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6125 (t0) REVERT: 5 307 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.5311 (pmt170) REVERT: 5 360 LYS cc_start: 0.2411 (mmtt) cc_final: 0.2159 (mmtp) REVERT: 5 379 ASP cc_start: 0.7318 (t70) cc_final: 0.6906 (t0) REVERT: 5 417 LYS cc_start: 0.7764 (pttt) cc_final: 0.7026 (mptt) REVERT: 5 468 LYS cc_start: 0.7112 (mmtm) cc_final: 0.6419 (mmmt) REVERT: 5 558 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.4900 (t80) REVERT: 5 562 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7879 (mp) REVERT: 5 588 MET cc_start: 0.6255 (tpp) cc_final: 0.5756 (ttm) REVERT: 5 641 ARG cc_start: 0.7090 (mmt180) cc_final: 0.6621 (mmm160) REVERT: 6 55 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4629 (pt) REVERT: 6 284 LEU cc_start: 0.3575 (OUTLIER) cc_final: 0.3016 (pp) REVERT: 6 296 GLN cc_start: 0.7710 (tp-100) cc_final: 0.6543 (tt0) REVERT: 6 309 MET cc_start: 0.4058 (mtp) cc_final: 0.2851 (ptm) REVERT: 6 332 MET cc_start: 0.3910 (mpp) cc_final: 0.3317 (tpt) REVERT: 6 442 MET cc_start: 0.7237 (mmm) cc_final: 0.6889 (mmm) REVERT: 6 584 HIS cc_start: 0.7104 (m90) cc_final: 0.6841 (t-170) REVERT: 7 83 GLU cc_start: 0.4701 (mm-30) cc_final: 0.3890 (tp30) REVERT: 7 93 VAL cc_start: 0.3880 (OUTLIER) cc_final: 0.3357 (p) REVERT: 7 215 LYS cc_start: 0.3743 (OUTLIER) cc_final: 0.2090 (tttp) REVERT: 7 223 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7862 (tp-100) REVERT: 7 248 HIS cc_start: 0.7591 (t-90) cc_final: 0.7110 (t70) REVERT: 7 256 MET cc_start: 0.7049 (tmm) cc_final: 0.6638 (mtt) REVERT: 7 266 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.5392 (mm-40) REVERT: 7 281 MET cc_start: 0.7901 (mtm) cc_final: 0.7142 (mtp) REVERT: 7 391 LEU cc_start: 0.8797 (tp) cc_final: 0.8353 (pp) REVERT: 7 494 ARG cc_start: 0.4921 (ptm-80) cc_final: 0.4049 (ttm170) REVERT: 7 527 ARG cc_start: 0.7585 (ttp80) cc_final: 0.6556 (mmt180) REVERT: 7 568 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7352 (ttp-170) REVERT: A 53 MET cc_start: 0.6406 (mpp) cc_final: 0.5293 (mtp) REVERT: A 201 MET cc_start: 0.6633 (tpp) cc_final: 0.6216 (tpt) REVERT: A 422 LYS cc_start: 0.4972 (mmtt) cc_final: 0.4744 (mmtt) REVERT: A 507 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6356 (mp) REVERT: H 61 ARG cc_start: 0.7416 (pmt-80) cc_final: 0.5985 (ptm-80) REVERT: H 130 MET cc_start: 0.6176 (mmm) cc_final: 0.5656 (tpp) REVERT: L 18 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7475 (mt) REVERT: L 93 MET cc_start: 0.5701 (mpp) cc_final: 0.4749 (tpp) REVERT: L 120 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.7941 (mm) REVERT: M 14 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5794 (mm-30) REVERT: M 81 HIS cc_start: 0.3712 (OUTLIER) cc_final: 0.3240 (t70) REVERT: M 101 PHE cc_start: 0.4714 (t80) cc_final: 0.4309 (t80) REVERT: M 173 MET cc_start: 0.7055 (pmm) cc_final: 0.6652 (pmm) REVERT: N 50 MET cc_start: 0.7697 (ttp) cc_final: 0.7480 (ttp) REVERT: N 172 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7337 (mp) outliers start: 226 outliers final: 163 residues processed: 806 average time/residue: 0.5290 time to fit residues: 691.0263 Evaluate side-chains 798 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 615 time to evaluate : 5.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 178 THR Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 211 ASN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 357 ASN Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 381 VAL Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 497 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 609 CYS Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 715 ILE Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 3 residue 11 ASP Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 65 ASN Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 210 LEU Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 258 LEU Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 291 PHE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 477 ASP Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 606 ILE Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 660 PHE Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 297 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 34 GLU Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 485 LEU Chi-restraints excluded: chain 6 residue 518 ILE Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 527 ILE Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 42 HIS Chi-restraints excluded: chain 7 residue 51 ASP Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 185 ASP Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 266 GLN Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 355 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 514 ARG Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 559 MET Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 89 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 172 ILE Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 440 optimal weight: 0.7980 chunk 463 optimal weight: 0.9980 chunk 422 optimal weight: 10.0000 chunk 450 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 407 optimal weight: 0.9980 chunk 426 optimal weight: 0.0870 chunk 449 optimal weight: 2.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 26 ASN ** 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** 6 115 HIS ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 165 GLN ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 564 ASN ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 HIS ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 41733 Z= 0.191 Angle : 0.701 13.046 56502 Z= 0.349 Chirality : 0.044 0.220 6362 Planarity : 0.005 0.066 7230 Dihedral : 11.111 139.751 6025 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.10 % Favored : 87.88 % Rotamer: Outliers : 4.49 % Allowed : 26.82 % Favored : 68.69 % 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: -3.24 (0.11), residues: 5000 helix: -0.81 (0.13), residues: 1638 sheet: -2.51 (0.21), residues: 546 loop : -3.04 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 6 326 HIS 0.015 0.001 HIS 6 115 PHE 0.038 0.002 PHE A 530 TYR 0.023 0.001 TYR 7 562 ARG 0.009 0.000 ARG 6 542 *********************** 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 834 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 635 time to evaluate : 4.647 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 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 revert: symmetry clash revert: symmetry clash REVERT: 2 212 MET cc_start: 0.6331 (mmt) cc_final: 0.5494 (mtm) REVERT: 2 350 MET cc_start: 0.3892 (mtt) cc_final: 0.2519 (tpp) REVERT: 2 351 GLU cc_start: 0.6136 (pm20) cc_final: 0.5725 (tp30) REVERT: 2 488 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6068 (mm-30) REVERT: 2 497 LYS cc_start: 0.5132 (OUTLIER) cc_final: 0.4921 (mptt) REVERT: 2 553 GLU cc_start: 0.6883 (mp0) cc_final: 0.5166 (tp30) REVERT: 2 605 LEU cc_start: 0.7389 (tp) cc_final: 0.7020 (tp) REVERT: 2 670 LYS cc_start: 0.5892 (pttp) cc_final: 0.5172 (mttp) REVERT: 2 693 PRO cc_start: 0.4329 (Cg_endo) cc_final: 0.4040 (Cg_exo) REVERT: 2 752 GLU cc_start: 0.5879 (pt0) cc_final: 0.5458 (pt0) REVERT: 3 36 MET cc_start: 0.4610 (ptm) cc_final: 0.4289 (mpp) REVERT: 3 140 ARG cc_start: 0.7154 (ptt180) cc_final: 0.6908 (ptt180) REVERT: 3 155 LYS cc_start: 0.7120 (tptp) cc_final: 0.6697 (tttt) REVERT: 3 253 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6028 (t80) REVERT: 3 268 GLU cc_start: 0.7916 (tp30) cc_final: 0.7607 (tp30) REVERT: 3 296 LYS cc_start: 0.6330 (mttt) cc_final: 0.5666 (pttt) REVERT: 3 364 THR cc_start: 0.5341 (OUTLIER) cc_final: 0.5006 (p) REVERT: 3 407 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8219 (p0) REVERT: 3 462 GLU cc_start: 0.8262 (tp30) cc_final: 0.7729 (tp30) REVERT: 3 466 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7234 (mt) REVERT: 3 530 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.4708 (mm-30) REVERT: 4 513 ASP cc_start: 0.6976 (m-30) cc_final: 0.5953 (p0) REVERT: 4 521 MET cc_start: 0.6685 (ppp) cc_final: 0.6198 (ppp) REVERT: 4 595 GLN cc_start: 0.7777 (mt0) cc_final: 0.7233 (mt0) REVERT: 4 630 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7472 (ttpp) REVERT: 4 676 ARG cc_start: 0.3411 (pmt-80) cc_final: 0.1787 (ptt90) REVERT: 4 680 GLU cc_start: 0.1877 (OUTLIER) cc_final: 0.0955 (mt-10) REVERT: 4 695 TYR cc_start: 0.8586 (t80) cc_final: 0.8328 (t80) REVERT: 5 70 GLU cc_start: 0.5918 (pp20) cc_final: 0.4756 (pp20) REVERT: 5 210 MET cc_start: 0.7525 (mmm) cc_final: 0.6788 (mmp) REVERT: 5 216 CYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7021 (p) REVERT: 5 226 GLU cc_start: 0.5807 (tm-30) cc_final: 0.5071 (tm-30) REVERT: 5 245 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.6086 (t0) REVERT: 5 307 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.5114 (pmt170) REVERT: 5 360 LYS cc_start: 0.2490 (mmtt) cc_final: 0.2252 (mmtp) REVERT: 5 379 ASP cc_start: 0.7273 (t70) cc_final: 0.6875 (t0) REVERT: 5 417 LYS cc_start: 0.7835 (pttt) cc_final: 0.7159 (mptt) REVERT: 5 468 LYS cc_start: 0.7285 (mmtm) cc_final: 0.6553 (mmmt) REVERT: 5 558 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.5163 (t80) REVERT: 5 562 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7827 (mp) REVERT: 5 588 MET cc_start: 0.6318 (tpp) cc_final: 0.5879 (tmm) REVERT: 5 641 ARG cc_start: 0.7106 (mmt180) cc_final: 0.6623 (mmm160) REVERT: 6 55 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.4904 (pt) REVERT: 6 101 GLN cc_start: 0.8190 (pp30) cc_final: 0.6493 (mt0) REVERT: 6 161 ASN cc_start: 0.5735 (p0) cc_final: 0.5284 (m-40) REVERT: 6 256 THR cc_start: 0.1513 (OUTLIER) cc_final: 0.1041 (p) REVERT: 6 284 LEU cc_start: 0.3720 (OUTLIER) cc_final: 0.3121 (pp) REVERT: 6 296 GLN cc_start: 0.7482 (tp-100) cc_final: 0.6310 (tt0) REVERT: 6 309 MET cc_start: 0.4012 (mtp) cc_final: 0.2775 (ptm) REVERT: 6 332 MET cc_start: 0.3773 (mpp) cc_final: 0.3409 (tpt) REVERT: 6 469 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.5186 (ppp) REVERT: 6 565 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.5099 (mm) REVERT: 6 584 HIS cc_start: 0.7087 (m90) cc_final: 0.6816 (t-170) REVERT: 7 83 GLU cc_start: 0.4680 (mm-30) cc_final: 0.3863 (tp30) REVERT: 7 93 VAL cc_start: 0.3647 (OUTLIER) cc_final: 0.3171 (p) REVERT: 7 215 LYS cc_start: 0.3656 (OUTLIER) cc_final: 0.2038 (tttp) REVERT: 7 223 GLN cc_start: 0.8349 (tp-100) cc_final: 0.7916 (tp-100) REVERT: 7 248 HIS cc_start: 0.7835 (t-90) cc_final: 0.7297 (t-90) REVERT: 7 256 MET cc_start: 0.6989 (tmm) cc_final: 0.6502 (mtt) REVERT: 7 281 MET cc_start: 0.7887 (mtm) cc_final: 0.7102 (mtp) REVERT: 7 391 LEU cc_start: 0.8701 (tp) cc_final: 0.8310 (pp) REVERT: 7 494 ARG cc_start: 0.4989 (ptm-80) cc_final: 0.4087 (ttm170) REVERT: 7 568 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7380 (ttp-170) REVERT: A 53 MET cc_start: 0.6458 (mpp) cc_final: 0.5385 (mtp) REVERT: A 201 MET cc_start: 0.6447 (tpp) cc_final: 0.6064 (tpt) REVERT: A 422 LYS cc_start: 0.5155 (mmtt) cc_final: 0.4864 (mmtt) REVERT: A 507 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6382 (mp) REVERT: H 61 ARG cc_start: 0.7429 (pmt-80) cc_final: 0.6765 (ptm-80) REVERT: H 68 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7942 (m-40) REVERT: H 130 MET cc_start: 0.6121 (mmm) cc_final: 0.5624 (tpp) REVERT: L 18 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7532 (mt) REVERT: L 93 MET cc_start: 0.5628 (mpp) cc_final: 0.4724 (tpp) REVERT: L 120 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7917 (mm) REVERT: M 14 GLU cc_start: 0.6292 (mm-30) cc_final: 0.5902 (mm-30) REVERT: M 81 HIS cc_start: 0.4084 (OUTLIER) cc_final: 0.3131 (t70) REVERT: M 101 PHE cc_start: 0.4405 (t80) cc_final: 0.4092 (t80) REVERT: M 173 MET cc_start: 0.7008 (pmm) cc_final: 0.6650 (pmm) REVERT: N 172 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7211 (mp) outliers start: 199 outliers final: 156 residues processed: 771 average time/residue: 0.5291 time to fit residues: 660.0620 Evaluate side-chains 794 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 613 time to evaluate : 4.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 178 THR Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 211 ASN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 460 GLU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 497 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 715 ILE Chi-restraints excluded: chain 2 residue 743 HIS Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 3 residue 11 ASP Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 280 LEU Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 291 PHE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 530 GLU Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 477 ASP Chi-restraints excluded: chain 4 residue 511 CYS Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 606 ILE Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 660 PHE Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 717 VAL Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 216 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 297 VAL Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 115 HIS Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 378 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 469 MET Chi-restraints excluded: chain 6 residue 485 LEU Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 42 HIS Chi-restraints excluded: chain 7 residue 51 ASP Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 185 ASP Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 251 ARG Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 355 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 514 ARG Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 69 PHE Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 172 ILE Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 296 optimal weight: 8.9990 chunk 476 optimal weight: 3.9990 chunk 291 optimal weight: 0.9990 chunk 226 optimal weight: 5.9990 chunk 331 optimal weight: 0.9980 chunk 500 optimal weight: 7.9990 chunk 460 optimal weight: 0.7980 chunk 398 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 307 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 329 ASN ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 348 GLN 3 567 HIS ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 26 ASN ** 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** ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 612 GLN 7 266 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** 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 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 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: 0.5814 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41733 Z= 0.198 Angle : 0.713 13.788 56502 Z= 0.354 Chirality : 0.045 0.243 6362 Planarity : 0.005 0.069 7230 Dihedral : 11.027 135.126 6025 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.60 % Favored : 87.38 % Rotamer: Outliers : 4.35 % Allowed : 27.09 % Favored : 68.55 % 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: -3.19 (0.11), residues: 5000 helix: -0.80 (0.13), residues: 1636 sheet: -2.45 (0.21), residues: 523 loop : -2.99 (0.11), residues: 2841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 64 HIS 0.010 0.001 HIS 5 115 PHE 0.037 0.002 PHE A 530 TYR 0.028 0.002 TYR 5 585 ARG 0.018 0.001 ARG M 130 ********************** 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 828 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 635 time to evaluate : 4.896 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 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 REVERT: 2 212 MET cc_start: 0.6211 (mmt) cc_final: 0.5425 (mtp) REVERT: 2 350 MET cc_start: 0.3869 (mtt) cc_final: 0.2572 (tpp) REVERT: 2 351 GLU cc_start: 0.6091 (pm20) cc_final: 0.5784 (tp30) REVERT: 2 461 ARG cc_start: 0.6511 (ttm170) cc_final: 0.6133 (ttt-90) REVERT: 2 488 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6263 (mm-30) REVERT: 2 494 GLU cc_start: 0.4892 (pp20) cc_final: 0.4507 (pp20) REVERT: 2 553 GLU cc_start: 0.6943 (mp0) cc_final: 0.5315 (tp30) REVERT: 2 554 TRP cc_start: 0.3406 (t-100) cc_final: 0.3176 (m-10) REVERT: 2 605 LEU cc_start: 0.7347 (tp) cc_final: 0.6979 (tp) REVERT: 2 670 LYS cc_start: 0.5966 (pttp) cc_final: 0.5249 (mttp) REVERT: 2 693 PRO cc_start: 0.4381 (Cg_endo) cc_final: 0.4108 (Cg_exo) REVERT: 2 752 GLU cc_start: 0.5973 (pt0) cc_final: 0.5607 (pt0) REVERT: 3 36 MET cc_start: 0.4728 (ptm) cc_final: 0.4414 (mpp) REVERT: 3 140 ARG cc_start: 0.7185 (ptt180) cc_final: 0.6887 (ptt180) REVERT: 3 155 LYS cc_start: 0.7153 (tptp) cc_final: 0.6729 (tttt) REVERT: 3 253 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6034 (t80) REVERT: 3 268 GLU cc_start: 0.8027 (tp30) cc_final: 0.7680 (tp30) REVERT: 3 296 LYS cc_start: 0.6383 (mttt) cc_final: 0.5722 (pttt) REVERT: 3 364 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.5016 (p) REVERT: 3 407 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8242 (p0) REVERT: 3 462 GLU cc_start: 0.8274 (tp30) cc_final: 0.7723 (tp30) REVERT: 3 466 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7374 (mt) REVERT: 3 530 GLU cc_start: 0.5231 (OUTLIER) cc_final: 0.4932 (mm-30) REVERT: 3 560 GLU cc_start: 0.6211 (tp30) cc_final: 0.5976 (tp30) REVERT: 4 513 ASP cc_start: 0.7107 (m-30) cc_final: 0.6109 (p0) REVERT: 4 595 GLN cc_start: 0.7780 (mt0) cc_final: 0.7304 (mt0) REVERT: 4 630 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7483 (ttpp) REVERT: 4 676 ARG cc_start: 0.3484 (pmt-80) cc_final: 0.1869 (ptt90) REVERT: 4 680 GLU cc_start: 0.1890 (OUTLIER) cc_final: 0.0982 (mt-10) REVERT: 4 695 TYR cc_start: 0.8564 (t80) cc_final: 0.8304 (t80) REVERT: 4 712 LEU cc_start: 0.7658 (tp) cc_final: 0.7314 (pp) REVERT: 5 70 GLU cc_start: 0.5938 (pp20) cc_final: 0.4727 (pp20) REVERT: 5 216 CYS cc_start: 0.7230 (p) cc_final: 0.6930 (p) REVERT: 5 226 GLU cc_start: 0.5799 (tm-30) cc_final: 0.5073 (tm-30) REVERT: 5 245 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6184 (t0) REVERT: 5 307 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.5094 (pmt170) REVERT: 5 368 ARG cc_start: 0.3496 (ptt180) cc_final: 0.2695 (mmt180) REVERT: 5 379 ASP cc_start: 0.7290 (t70) cc_final: 0.6862 (t0) REVERT: 5 417 LYS cc_start: 0.7931 (pttt) cc_final: 0.7210 (mptt) REVERT: 5 468 LYS cc_start: 0.7208 (mmtm) cc_final: 0.6489 (mmmt) REVERT: 5 558 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.5222 (t80) REVERT: 5 562 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (mp) REVERT: 5 588 MET cc_start: 0.5973 (tpp) cc_final: 0.5731 (tmm) REVERT: 5 589 ARG cc_start: 0.4313 (tpt90) cc_final: 0.3972 (mtp180) REVERT: 5 641 ARG cc_start: 0.7141 (mmt180) cc_final: 0.6651 (mmm160) REVERT: 6 55 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4873 (pt) REVERT: 6 101 GLN cc_start: 0.8154 (pp30) cc_final: 0.6474 (mt0) REVERT: 6 161 ASN cc_start: 0.5841 (p0) cc_final: 0.5403 (m-40) REVERT: 6 256 THR cc_start: 0.1527 (OUTLIER) cc_final: 0.1071 (p) REVERT: 6 284 LEU cc_start: 0.3622 (OUTLIER) cc_final: 0.2994 (pp) REVERT: 6 309 MET cc_start: 0.3879 (mtp) cc_final: 0.2803 (ptm) REVERT: 6 332 MET cc_start: 0.3793 (mpp) cc_final: 0.3457 (tpt) REVERT: 6 469 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.5089 (ppp) REVERT: 6 565 LEU cc_start: 0.5613 (OUTLIER) cc_final: 0.5289 (mm) REVERT: 7 83 GLU cc_start: 0.4675 (mm-30) cc_final: 0.3866 (tp30) REVERT: 7 93 VAL cc_start: 0.3540 (OUTLIER) cc_final: 0.2991 (p) REVERT: 7 215 LYS cc_start: 0.3634 (OUTLIER) cc_final: 0.2022 (tttp) REVERT: 7 223 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7799 (tp-100) REVERT: 7 248 HIS cc_start: 0.7838 (t-90) cc_final: 0.7105 (t-90) REVERT: 7 256 MET cc_start: 0.7015 (tmm) cc_final: 0.6523 (mtt) REVERT: 7 266 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5033 (mm-40) REVERT: 7 281 MET cc_start: 0.7869 (mtm) cc_final: 0.7109 (mtp) REVERT: 7 391 LEU cc_start: 0.8672 (tp) cc_final: 0.8362 (pp) REVERT: 7 494 ARG cc_start: 0.4967 (ptm-80) cc_final: 0.4157 (ttm170) REVERT: 7 527 ARG cc_start: 0.7728 (ptm-80) cc_final: 0.7489 (ttp80) REVERT: 7 568 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7423 (ttp-170) REVERT: A 53 MET cc_start: 0.6313 (mpp) cc_final: 0.5313 (mtp) REVERT: A 201 MET cc_start: 0.6437 (tpp) cc_final: 0.6080 (tpt) REVERT: A 422 LYS cc_start: 0.5070 (mmtt) cc_final: 0.4796 (mmtt) REVERT: A 507 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6404 (mp) REVERT: H 61 ARG cc_start: 0.7617 (pmt-80) cc_final: 0.6916 (ptm-80) REVERT: H 130 MET cc_start: 0.6183 (mmm) cc_final: 0.5808 (tpp) REVERT: L 18 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7464 (mt) REVERT: L 93 MET cc_start: 0.5674 (mpp) cc_final: 0.4803 (tpp) REVERT: L 120 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.7904 (mm) REVERT: M 14 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5903 (mm-30) REVERT: M 81 HIS cc_start: 0.4102 (OUTLIER) cc_final: 0.3265 (t70) REVERT: M 173 MET cc_start: 0.7068 (pmm) cc_final: 0.6720 (pmm) REVERT: N 172 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7225 (mp) outliers start: 193 outliers final: 151 residues processed: 773 average time/residue: 0.5364 time to fit residues: 669.4406 Evaluate side-chains 779 residues out of total 4447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 605 time to evaluate : 4.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 178 THR Chi-restraints excluded: chain 2 residue 187 PHE Chi-restraints excluded: chain 2 residue 211 ASN Chi-restraints excluded: chain 2 residue 266 ILE Chi-restraints excluded: chain 2 residue 296 VAL Chi-restraints excluded: chain 2 residue 309 VAL Chi-restraints excluded: chain 2 residue 314 CYS Chi-restraints excluded: chain 2 residue 366 SER Chi-restraints excluded: chain 2 residue 391 CYS Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 419 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 463 VAL Chi-restraints excluded: chain 2 residue 476 ILE Chi-restraints excluded: chain 2 residue 489 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 548 ASN Chi-restraints excluded: chain 2 residue 561 LEU Chi-restraints excluded: chain 2 residue 562 VAL Chi-restraints excluded: chain 2 residue 585 ILE Chi-restraints excluded: chain 2 residue 709 ARG Chi-restraints excluded: chain 2 residue 715 ILE Chi-restraints excluded: chain 2 residue 743 HIS Chi-restraints excluded: chain 2 residue 744 ILE Chi-restraints excluded: chain 2 residue 754 HIS Chi-restraints excluded: chain 3 residue 11 ASP Chi-restraints excluded: chain 3 residue 40 LYS Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 105 ASN Chi-restraints excluded: chain 3 residue 116 ILE Chi-restraints excluded: chain 3 residue 123 CYS Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 253 PHE Chi-restraints excluded: chain 3 residue 260 ASN Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 277 ASP Chi-restraints excluded: chain 3 residue 280 LEU Chi-restraints excluded: chain 3 residue 284 LEU Chi-restraints excluded: chain 3 residue 291 PHE Chi-restraints excluded: chain 3 residue 302 ILE Chi-restraints excluded: chain 3 residue 348 GLN Chi-restraints excluded: chain 3 residue 364 THR Chi-restraints excluded: chain 3 residue 407 ASP Chi-restraints excluded: chain 3 residue 466 LEU Chi-restraints excluded: chain 3 residue 530 GLU Chi-restraints excluded: chain 3 residue 647 TYR Chi-restraints excluded: chain 4 residue 211 LEU Chi-restraints excluded: chain 4 residue 218 LEU Chi-restraints excluded: chain 4 residue 306 PHE Chi-restraints excluded: chain 4 residue 325 ILE Chi-restraints excluded: chain 4 residue 357 LEU Chi-restraints excluded: chain 4 residue 363 ASP Chi-restraints excluded: chain 4 residue 392 THR Chi-restraints excluded: chain 4 residue 393 VAL Chi-restraints excluded: chain 4 residue 397 TYR Chi-restraints excluded: chain 4 residue 419 VAL Chi-restraints excluded: chain 4 residue 477 ASP Chi-restraints excluded: chain 4 residue 585 THR Chi-restraints excluded: chain 4 residue 590 HIS Chi-restraints excluded: chain 4 residue 592 VAL Chi-restraints excluded: chain 4 residue 606 ILE Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 663 ARG Chi-restraints excluded: chain 4 residue 680 GLU Chi-restraints excluded: chain 4 residue 683 MET Chi-restraints excluded: chain 4 residue 717 VAL Chi-restraints excluded: chain 4 residue 771 LEU Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 94 PHE Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 139 CYS Chi-restraints excluded: chain 5 residue 151 VAL Chi-restraints excluded: chain 5 residue 202 CYS Chi-restraints excluded: chain 5 residue 217 VAL Chi-restraints excluded: chain 5 residue 245 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 263 ILE Chi-restraints excluded: chain 5 residue 307 ARG Chi-restraints excluded: chain 5 residue 336 LEU Chi-restraints excluded: chain 5 residue 382 THR Chi-restraints excluded: chain 5 residue 431 MET Chi-restraints excluded: chain 5 residue 556 SER Chi-restraints excluded: chain 5 residue 558 PHE Chi-restraints excluded: chain 5 residue 562 ILE Chi-restraints excluded: chain 5 residue 567 THR Chi-restraints excluded: chain 5 residue 643 PHE Chi-restraints excluded: chain 5 residue 652 MET Chi-restraints excluded: chain 6 residue 17 VAL Chi-restraints excluded: chain 6 residue 34 GLU Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 55 LEU Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 123 SER Chi-restraints excluded: chain 6 residue 169 THR Chi-restraints excluded: chain 6 residue 256 THR Chi-restraints excluded: chain 6 residue 284 LEU Chi-restraints excluded: chain 6 residue 299 THR Chi-restraints excluded: chain 6 residue 338 LEU Chi-restraints excluded: chain 6 residue 378 LEU Chi-restraints excluded: chain 6 residue 403 ASP Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 469 MET Chi-restraints excluded: chain 6 residue 485 LEU Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 555 VAL Chi-restraints excluded: chain 6 residue 565 LEU Chi-restraints excluded: chain 6 residue 585 MET Chi-restraints excluded: chain 7 residue 37 LEU Chi-restraints excluded: chain 7 residue 42 HIS Chi-restraints excluded: chain 7 residue 51 ASP Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 93 VAL Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 185 ASP Chi-restraints excluded: chain 7 residue 196 ASN Chi-restraints excluded: chain 7 residue 215 LYS Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 257 CYS Chi-restraints excluded: chain 7 residue 266 GLN Chi-restraints excluded: chain 7 residue 319 LEU Chi-restraints excluded: chain 7 residue 355 LEU Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 461 VAL Chi-restraints excluded: chain 7 residue 549 THR Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 80 CYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 156 VAL Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 81 HIS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 131 HIS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 172 ILE Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 316 optimal weight: 8.9990 chunk 424 optimal weight: 0.0980 chunk 122 optimal weight: 0.8980 chunk 367 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 110 optimal weight: 0.0970 chunk 398 optimal weight: 0.5980 chunk 166 optimal weight: 0.0670 chunk 409 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 658 GLN ** 2 671 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** ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 26 ASN ** 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 67 GLN ** 6 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 584 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** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS N 110 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.269237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.255102 restraints weight = 73859.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.254598 restraints weight = 98270.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.255354 restraints weight = 86964.238| |-----------------------------------------------------------------------------| r_work (final): 0.5004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.318 41733 Z= 0.308 Angle : 0.805 59.200 56502 Z= 0.415 Chirality : 0.045 0.536 6362 Planarity : 0.005 0.088 7230 Dihedral : 11.001 133.918 6022 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.86 % Favored : 87.12 % Rotamer: Outliers : 4.31 % Allowed : 27.34 % Favored : 68.35 % Cbeta Deviations : 0.02 % 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: -3.18 (0.11), residues: 5000 helix: -0.81 (0.13), residues: 1637 sheet: -2.44 (0.21), residues: 523 loop : -2.98 (0.11), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 4 155 HIS 0.015 0.001 HIS 7 248 PHE 0.063 0.002 PHE M 101 TYR 0.024 0.001 TYR 5 585 ARG 0.009 0.000 ARG M 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11967.21 seconds wall clock time: 214 minutes 22.90 seconds (12862.90 seconds total)