Starting phenix.real_space_refine on Sat Jan 20 01:26:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skl_10227/01_2024/6skl_10227_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skl_10227/01_2024/6skl_10227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skl_10227/01_2024/6skl_10227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skl_10227/01_2024/6skl_10227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skl_10227/01_2024/6skl_10227_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skl_10227/01_2024/6skl_10227_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 5 6.06 5 P 68 5.49 5 Mg 3 5.21 5 S 253 5.16 5 C 37405 2.51 5 N 10159 2.21 5 O 11291 1.98 5 H 58997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 217": "OE1" <-> "OE2" Residue "2 GLU 243": "OE1" <-> "OE2" Residue "2 ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 292": "OE1" <-> "OE2" Residue "2 GLU 311": "OE1" <-> "OE2" Residue "2 ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 357": "OE1" <-> "OE2" Residue "2 ARG 360": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 378": "OE1" <-> "OE2" Residue "2 GLU 392": "OE1" <-> "OE2" Residue "2 GLU 422": "OE1" <-> "OE2" Residue "2 GLU 452": "OE1" <-> "OE2" Residue "2 ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 460": "OE1" <-> "OE2" Residue "2 GLU 466": "OE1" <-> "OE2" Residue "2 GLU 468": "OE1" <-> "OE2" Residue "2 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 GLU 478": "OE1" <-> "OE2" Residue "2 GLU 479": "OE1" <-> "OE2" Residue "2 GLU 483": "OE1" <-> "OE2" Residue "2 ARG 489": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 581": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 622": "OE1" <-> "OE2" Residue "2 ARG 656": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 689": "OE1" <-> "OE2" Residue "2 ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 741": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 747": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 749": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 754": "OE1" <-> "OE2" Residue "2 GLU 761": "OE1" <-> "OE2" Residue "2 ARG 794": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 808": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 818": "OE1" <-> "OE2" Residue "2 ARG 824": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 827": "OE1" <-> "OE2" Residue "2 ARG 854": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "3 ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 108": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 117": "OE1" <-> "OE2" Residue "3 GLU 183": "OE1" <-> "OE2" Residue "3 ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 234": "OE1" <-> "OE2" Residue "3 GLU 237": "OE1" <-> "OE2" Residue "3 GLU 260": "OE1" <-> "OE2" Residue "3 ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 390": "OE1" <-> "OE2" Residue "3 GLU 394": "OE1" <-> "OE2" Residue "3 ARG 420": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 435": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 451": "OE1" <-> "OE2" Residue "3 GLU 458": "OE1" <-> "OE2" Residue "3 ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 491": "OE1" <-> "OE2" Residue "3 ASP 544": "OD1" <-> "OD2" Residue "3 GLU 578": "OE1" <-> "OE2" Residue "3 ARG 657": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 700": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 740": "OE1" <-> "OE2" Residue "4 ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 213": "OE1" <-> "OE2" Residue "4 ARG 234": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 359": "OE1" <-> "OE2" Residue "4 ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 401": "OE1" <-> "OE2" Residue "4 ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 434": "OE1" <-> "OE2" Residue "4 ARG 449": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 451": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 534": "OE1" <-> "OE2" Residue "4 ARG 557": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 559": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 587": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 681": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 806": "OE1" <-> "OE2" Residue "4 GLU 818": "OE1" <-> "OE2" Residue "4 GLU 820": "OE1" <-> "OE2" Residue "4 ARG 827": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 863": "OE1" <-> "OE2" Residue "4 GLU 868": "OE1" <-> "OE2" Residue "4 GLU 885": "OE1" <-> "OE2" Residue "4 ARG 897": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 905": "OE1" <-> "OE2" Residue "5 GLU 66": "OE1" <-> "OE2" Residue "5 GLU 82": "OE1" <-> "OE2" Residue "5 ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 154": "OE1" <-> "OE2" Residue "5 TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 GLU 338": "OE1" <-> "OE2" Residue "5 GLU 354": "OE1" <-> "OE2" Residue "5 GLU 355": "OE1" <-> "OE2" Residue "5 GLU 356": "OE1" <-> "OE2" Residue "5 ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ARG 460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 465": "OE1" <-> "OE2" Residue "5 GLU 488": "OE1" <-> "OE2" Residue "5 GLU 498": "OE1" <-> "OE2" Residue "5 GLU 593": "OE1" <-> "OE2" Residue "5 GLU 597": "OE1" <-> "OE2" Residue "5 GLU 642": "OE1" <-> "OE2" Residue "5 ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 667": "OE1" <-> "OE2" Residue "5 GLU 674": "OE1" <-> "OE2" Residue "6 GLU 109": "OE1" <-> "OE2" Residue "6 GLU 113": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 275": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 360": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 387": "OE1" <-> "OE2" Residue "6 ARG 446": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 498": "OE1" <-> "OE2" Residue "6 ARG 531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 624": "OE1" <-> "OE2" Residue "6 ARG 691": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 696": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 708": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 768": "OE1" <-> "OE2" Residue "6 ARG 781": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 808": "OE1" <-> "OE2" Residue "6 GLU 826": "OE1" <-> "OE2" Residue "7 GLU 131": "OE1" <-> "OE2" Residue "7 ARG 199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 373": "OE1" <-> "OE2" Residue "7 GLU 398": "OE1" <-> "OE2" Residue "7 GLU 399": "OE1" <-> "OE2" Residue "7 ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 451": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 539": "OE1" <-> "OE2" Residue "7 GLU 542": "OE1" <-> "OE2" Residue "7 ARG 573": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 640": "OE1" <-> "OE2" Residue "7 ARG 666": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 673": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 703": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 718": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 142": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 264": "OE1" <-> "OE2" Residue "E ARG 386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 398": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 411": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 504": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 558": "OE1" <-> "OE2" Residue "E ARG 587": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 631": "OE1" <-> "OE2" Residue "E ARG 633": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 610": "OE1" <-> "OE2" Residue "F ARG 649": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 714": "OE1" <-> "OE2" Residue "F GLU 727": "OE1" <-> "OE2" Residue "F GLU 736": "OE1" <-> "OE2" Residue "F GLU 814": "OE1" <-> "OE2" Residue "F GLU 824": "OE1" <-> "OE2" Residue "F TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 888": "OE1" <-> "OE2" Residue "G ARG 522": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 529": "OE1" <-> "OE2" Residue "G GLU 541": "OE1" <-> "OE2" Residue "G GLU 642": "OE1" <-> "OE2" Residue "G ARG 649": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 715": "OE1" <-> "OE2" Residue "G GLU 788": "OE1" <-> "OE2" Residue "G GLU 814": "OE1" <-> "OE2" Residue "G GLU 824": "OE1" <-> "OE2" Residue "G GLU 835": "OE1" <-> "OE2" Residue "G GLU 906": "OE1" <-> "OE2" Residue "G GLU 923": "OE1" <-> "OE2" Residue "H GLU 509": "OE1" <-> "OE2" Residue "H PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 649": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 715": "OE1" <-> "OE2" Residue "H GLU 775": "OE1" <-> "OE2" Residue "H GLU 824": "OE1" <-> "OE2" Residue "H GLU 835": "OE1" <-> "OE2" Residue "H TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 880": "OE1" <-> "OE2" Residue "H GLU 888": "OE1" <-> "OE2" Residue "H ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 903": "OE1" <-> "OE2" Residue "H ARG 904": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 80": "OE1" <-> "OE2" Residue "X ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 155": "OE1" <-> "OE2" Residue "X ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 288": "OE1" <-> "OE2" Residue "X PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 342": "OE1" <-> "OE2" Residue "X ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 385": "OE1" <-> "OE2" Residue "X GLU 412": "OE1" <-> "OE2" Residue "X GLU 431": "OE1" <-> "OE2" Residue "X ARG 466": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 507": "OE1" <-> "OE2" Residue "X ARG 563": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 673": "OE1" <-> "OE2" Residue "X PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 118181 Number of models: 1 Model: "" Number of chains: 24 Chain: "2" Number of atoms: 10572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 10572 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "3" Number of atoms: 9707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 9707 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 29, 'TRANS': 586} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "4" Number of atoms: 10882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 10882 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 23, 'TRANS': 655} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 9676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 9676 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 24, 'TRANS': 586} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 10044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 10044 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 23, 'TRANS': 613} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 9980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 9980 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 30, 'TRANS': 604} Chain breaks: 7 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3227 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 193} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3292 Classifications: {'peptide': 193} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2858 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 4008 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 9129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 9129 Classifications: {'peptide': 564} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 548} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 6759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6759 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 6693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6693 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 6769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 6769 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1192 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "J" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 686 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "X" Number of atoms: 10990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10990 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 20, 'TRANS': 644} Chain breaks: 7 Chain: "Y" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1616 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2686 SG CYS 2 341 103.475 114.831 85.490 1.00 0.00 S ATOM 2738 SG CYS 2 344 106.179 115.287 83.225 1.00 0.00 S ATOM 3043 SG CYS 2 364 106.355 117.178 86.495 1.00 0.00 S ATOM 3082 SG CYS 2 367 104.239 117.925 83.626 1.00 0.00 S ATOM 23170 SG CYS 4 349 88.451 149.206 97.544 1.00101.09 S ATOM 23211 SG CYS 4 352 88.810 152.573 98.198 1.00 96.38 S ATOM 23500 SG CYS 4 371 86.148 151.670 96.126 1.00110.38 S ATOM 23581 SG CYS 4 376 89.531 151.813 94.662 1.00117.84 S ATOM 33455 SG CYS 5 183 86.011 102.289 72.975 1.00 30.00 S ATOM 33504 SG CYS 5 186 87.197 101.901 69.350 1.00 83.56 S ATOM 33796 SG CYS 5 211 89.307 102.666 72.050 1.00 81.84 S ATOM 33851 SG CYS 5 236 87.028 105.091 71.601 1.00 30.00 S ATOM 43564 SG CYS 6 311 104.652 132.406 94.552 1.00 80.21 S ATOM 43604 SG CYS 6 314 107.296 134.503 93.664 1.00 79.97 S ATOM 43909 SG CYS 6 333 104.358 136.212 94.047 1.00 77.95 S ATOM 43973 SG CYS 6 338 104.720 134.212 91.066 1.00 91.55 S ATOM 53925 SG CYS 7 262 63.435 141.066 83.453 1.00 92.80 S ATOM 53965 SG CYS 7 265 61.443 141.730 80.802 1.00 96.91 S ATOM 54251 SG CYS 7 284 63.258 138.637 80.922 1.00105.78 S ATOM 54317 SG CYS 7 289 65.163 141.569 79.864 1.00118.44 S Time building chain proxies: 37.25, per 1000 atoms: 0.32 Number of scatterers: 118181 At special positions: 0 Unit cell: (224.486, 206.653, 196.163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 S 253 16.00 P 68 15.00 Mg 3 11.99 O 11291 8.00 N 10159 7.00 C 37405 6.00 H 58997 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 68.67 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 367 " pdb=" ZN 41400 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 376 " pdb=" ZN 5 803 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 183 " pdb=" ZN 61400 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 333 " pdb=" ZN 71400 " pdb="ZN ZN 71400 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 71400 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 71400 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 71400 " - pdb=" SG CYS 7 289 " Number of angles added : 30 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13838 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 253 helices and 71 sheets defined 49.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 46.00 Creating SS restraints... Processing helix chain '2' and resid 182 through 189 removed outlier: 4.279A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL 2 189 " --> pdb=" O SER 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 removed outlier: 3.585A pdb=" N THR 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 225 through 238 Processing helix chain '2' and resid 245 through 253 removed outlier: 3.802A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS 2 253 " --> pdb=" O LEU 2 249 " (cutoff:3.500A) Processing helix chain '2' and resid 254 through 263 Processing helix chain '2' and resid 265 through 284 removed outlier: 4.259A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Proline residue: 2 284 - end of helix Processing helix chain '2' and resid 285 through 290 removed outlier: 4.292A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 398 Proline residue: 2 398 - end of helix Processing helix chain '2' and resid 435 through 443 removed outlier: 3.708A pdb=" N ASN 2 439 " --> pdb=" O ASP 2 435 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 491 removed outlier: 3.774A pdb=" N GLU 2 483 " --> pdb=" O GLU 2 479 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP 2 490 " --> pdb=" O LYS 2 486 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG 2 491 " --> pdb=" O ILE 2 487 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 503 removed outlier: 5.748A pdb=" N ALA 2 502 " --> pdb=" O ILE 2 498 " (cutoff:3.500A) Proline residue: 2 503 - end of helix Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 572 through 578 removed outlier: 4.358A pdb=" N THR 2 577 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA 2 578 " --> pdb=" O VAL 2 574 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 600 removed outlier: 3.974A pdb=" N ASP 2 600 " --> pdb=" O LEU 2 596 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 626 removed outlier: 4.425A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N HIS 2 621 " --> pdb=" O ARG 2 617 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU 2 622 " --> pdb=" O THR 2 618 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA 2 623 " --> pdb=" O SER 2 619 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU 2 625 " --> pdb=" O HIS 2 621 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 668 removed outlier: 5.705A pdb=" N SER 2 668 " --> pdb=" O ALA 2 664 " (cutoff:3.500A) Processing helix chain '2' and resid 670 through 678 removed outlier: 3.729A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 673 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP 2 678 " --> pdb=" O LEU 2 674 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 707 removed outlier: 4.132A pdb=" N GLU 2 693 " --> pdb=" O GLU 2 689 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 756 removed outlier: 4.711A pdb=" N LEU 2 745 " --> pdb=" O ARG 2 741 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN 2 746 " --> pdb=" O GLN 2 742 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG 2 747 " --> pdb=" O ARG 2 743 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE 2 755 " --> pdb=" O LYS 2 751 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 773 removed outlier: 3.546A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 798 removed outlier: 3.769A pdb=" N ILE 2 798 " --> pdb=" O ARG 2 794 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 825 removed outlier: 3.585A pdb=" N SER 2 812 " --> pdb=" O ARG 2 808 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.762A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 850 through 862 removed outlier: 4.231A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 36 removed outlier: 3.625A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 53 Processing helix chain '3' and resid 99 through 107 Processing helix chain '3' and resid 108 through 117 Processing helix chain '3' and resid 118 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 143 through 149 Processing helix chain '3' and resid 216 through 221 removed outlier: 3.729A pdb=" N THR 3 220 " --> pdb=" O ASP 3 216 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU 3 221 " --> pdb=" O ALA 3 217 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 216 through 221' Processing helix chain '3' and resid 261 through 266 removed outlier: 3.596A pdb=" N ALA 3 265 " --> pdb=" O MET 3 261 " (cutoff:3.500A) Proline residue: 3 266 - end of helix No H-bonds generated for 'chain '3' and resid 261 through 266' Processing helix chain '3' and resid 343 through 356 removed outlier: 3.821A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 369 removed outlier: 5.525A pdb=" N ALA 3 368 " --> pdb=" O SER 3 364 " (cutoff:3.500A) Proline residue: 3 369 - end of helix Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 removed outlier: 3.649A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN 3 424 " --> pdb=" O ARG 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 Processing helix chain '3' and resid 460 through 466 removed outlier: 4.048A pdb=" N ASP 3 466 " --> pdb=" O MET 3 462 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 492 removed outlier: 4.282A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE 3 486 " --> pdb=" O ASP 3 482 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 removed outlier: 5.956A pdb=" N ALA 3 534 " --> pdb=" O HIS 3 530 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 544 removed outlier: 3.564A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP 3 544 " --> pdb=" O LEU 3 540 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 571 removed outlier: 3.680A pdb=" N TYR 3 571 " --> pdb=" O ARG 3 567 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 666 Processing helix chain '3' and resid 672 through 689 removed outlier: 3.579A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS 3 681 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP 3 689 " --> pdb=" O ASP 3 685 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 4.076A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 186 through 200 removed outlier: 3.934A pdb=" N ASN 4 196 " --> pdb=" O THR 4 192 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER 4 200 " --> pdb=" O ASN 4 196 " (cutoff:3.500A) Processing helix chain '4' and resid 202 through 211 removed outlier: 4.532A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU 4 211 " --> pdb=" O LYS 4 207 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 244 through 252 removed outlier: 4.557A pdb=" N LEU 4 248 " --> pdb=" O ASP 4 244 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS 4 252 " --> pdb=" O LEU 4 248 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.739A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 288 removed outlier: 3.554A pdb=" N GLN 4 274 " --> pdb=" O SER 4 270 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 300 removed outlier: 4.046A pdb=" N ILE 4 296 " --> pdb=" O ASP 4 292 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS 4 299 " --> pdb=" O GLU 4 295 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE 4 300 " --> pdb=" O ILE 4 296 " (cutoff:3.500A) Processing helix chain '4' and resid 385 through 390 removed outlier: 5.590A pdb=" N SER 4 390 " --> pdb=" O HIS 4 386 " (cutoff:3.500A) Processing helix chain '4' and resid 505 through 514 removed outlier: 4.086A pdb=" N ILE 4 509 " --> pdb=" O ASP 4 505 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL 4 512 " --> pdb=" O LYS 4 508 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 528 removed outlier: 4.525A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Proline residue: 4 528 - end of helix Processing helix chain '4' and resid 533 through 546 removed outlier: 3.926A pdb=" N LEU 4 542 " --> pdb=" O LYS 4 538 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 597 through 603 Processing helix chain '4' and resid 638 through 651 removed outlier: 3.839A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 702 removed outlier: 3.826A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 727 removed outlier: 5.158A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS 4 722 " --> pdb=" O ARG 4 718 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN 4 726 " --> pdb=" O LYS 4 722 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 758 removed outlier: 5.743A pdb=" N THR 4 748 " --> pdb=" O VAL 4 744 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 780 removed outlier: 3.514A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 813 removed outlier: 4.004A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 834 removed outlier: 4.274A pdb=" N GLU 4 824 " --> pdb=" O GLU 4 820 " (cutoff:3.500A) Processing helix chain '4' and resid 851 through 876 removed outlier: 5.206A pdb=" N ILE 4 857 " --> pdb=" O GLY 4 853 " (cutoff:3.500A) Processing helix chain '4' and resid 882 through 891 Processing helix chain '4' and resid 899 through 914 removed outlier: 3.559A pdb=" N ILE 4 903 " --> pdb=" O GLU 4 899 " (cutoff:3.500A) Processing helix chain '4' and resid 217 through 222 removed outlier: 4.137A pdb=" N GLU 4 222 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 217 through 222' Processing helix chain '5' and resid 20 through 37 removed outlier: 3.561A pdb=" N PHE 5 34 " --> pdb=" O SER 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 57 removed outlier: 3.725A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 73 through 83 Proline residue: 5 83 - end of helix Processing helix chain '5' and resid 84 through 103 Proline residue: 5 88 - end of helix removed outlier: 3.676A pdb=" N THR 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) Processing helix chain '5' and resid 350 through 363 removed outlier: 4.270A pdb=" N GLU 5 356 " --> pdb=" O GLU 5 352 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 376 removed outlier: 5.556A pdb=" N ALA 5 375 " --> pdb=" O THR 5 371 " (cutoff:3.500A) Proline residue: 5 376 - end of helix Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 removed outlier: 4.122A pdb=" N LYS 5 431 " --> pdb=" O LYS 5 427 " (cutoff:3.500A) Processing helix chain '5' and resid 440 through 445 removed outlier: 5.538A pdb=" N SER 5 445 " --> pdb=" O GLY 5 441 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 473 Processing helix chain '5' and resid 486 through 499 removed outlier: 3.657A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 541 removed outlier: 3.982A pdb=" N ILE 5 540 " --> pdb=" O PRO 5 536 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASP 5 541 " --> pdb=" O GLY 5 537 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 551 removed outlier: 4.204A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASP 5 551 " --> pdb=" O LEU 5 547 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 578 removed outlier: 3.501A pdb=" N GLY 5 578 " --> pdb=" O ASN 5 574 " (cutoff:3.500A) Processing helix chain '5' and resid 579 through 591 Processing helix chain '5' and resid 595 through 610 removed outlier: 3.819A pdb=" N LEU 5 608 " --> pdb=" O THR 5 604 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 641 removed outlier: 3.612A pdb=" N ALA 5 619 " --> pdb=" O SER 5 615 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 668 removed outlier: 3.704A pdb=" N ALA 5 664 " --> pdb=" O THR 5 660 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 694 removed outlier: 4.037A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN 5 694 " --> pdb=" O ASP 5 690 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 121 Processing helix chain '6' and resid 134 through 147 removed outlier: 3.696A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 154 through 162 removed outlier: 3.544A pdb=" N LEU 6 158 " --> pdb=" O ASP 6 154 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 174 through 193 Proline residue: 6 179 - end of helix removed outlier: 3.704A pdb=" N ARG 6 187 " --> pdb=" O LYS 6 183 " (cutoff:3.500A) Processing helix chain '6' and resid 406 through 411 removed outlier: 3.898A pdb=" N LEU 6 410 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY 6 411 " --> pdb=" O VAL 6 407 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 406 through 411' Processing helix chain '6' and resid 500 through 509 removed outlier: 4.417A pdb=" N ASN 6 506 " --> pdb=" O GLU 6 502 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N SER 6 509 " --> pdb=" O LEU 6 505 " (cutoff:3.500A) Processing helix chain '6' and resid 510 through 522 removed outlier: 4.419A pdb=" N GLU 6 515 " --> pdb=" O ASP 6 511 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 534 removed outlier: 6.200A pdb=" N ALA 6 534 " --> pdb=" O VAL 6 530 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 removed outlier: 3.871A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 626 through 632 removed outlier: 3.731A pdb=" N ASP 6 632 " --> pdb=" O LEU 6 628 " (cutoff:3.500A) Processing helix chain '6' and resid 645 through 658 removed outlier: 4.705A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE 6 652 " --> pdb=" O ASP 6 648 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS 6 653 " --> pdb=" O GLN 6 649 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 removed outlier: 3.779A pdb=" N ASN 6 698 " --> pdb=" O SER 6 694 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU 6 699 " --> pdb=" O LEU 6 695 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 694 through 699' Processing helix chain '6' and resid 702 through 709 removed outlier: 4.002A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE 6 709 " --> pdb=" O ILE 6 705 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 737 removed outlier: 3.783A pdb=" N HIS 6 735 " --> pdb=" O ILE 6 731 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET 6 736 " --> pdb=" O VAL 6 732 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 761 removed outlier: 3.959A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE 6 761 " --> pdb=" O TYR 6 757 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 785 removed outlier: 3.749A pdb=" N VAL 6 774 " --> pdb=" O ARG 6 770 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA 6 785 " --> pdb=" O ARG 6 781 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.792A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 836 removed outlier: 3.756A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 28 Processing helix chain '7' and resid 61 through 73 Processing helix chain '7' and resid 81 through 96 removed outlier: 3.771A pdb=" N ILE 7 85 " --> pdb=" O ASP 7 81 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN 7 87 " --> pdb=" O ASP 7 83 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 109 removed outlier: 3.768A pdb=" N GLN 7 108 " --> pdb=" O SER 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 125 removed outlier: 3.507A pdb=" N THR 7 114 " --> pdb=" O ALA 7 110 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 156 removed outlier: 4.133A pdb=" N VAL 7 141 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP 7 156 " --> pdb=" O ARG 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 199 removed outlier: 4.502A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG 7 199 " --> pdb=" O ASN 7 195 " (cutoff:3.500A) Processing helix chain '7' and resid 219 through 224 removed outlier: 4.015A pdb=" N LYS 7 223 " --> pdb=" O ALA 7 219 " (cutoff:3.500A) Proline residue: 7 224 - end of helix No H-bonds generated for 'chain '7' and resid 219 through 224' Processing helix chain '7' and resid 286 through 293 removed outlier: 3.688A pdb=" N ASN 7 292 " --> pdb=" O GLU 7 288 " (cutoff:3.500A) Processing helix chain '7' and resid 362 through 369 removed outlier: 3.943A pdb=" N LEU 7 366 " --> pdb=" O GLY 7 362 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS 7 367 " --> pdb=" O PHE 7 363 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY 7 369 " --> pdb=" O ALA 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 397 through 408 removed outlier: 3.709A pdb=" N VAL 7 401 " --> pdb=" O VAL 7 397 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N MET 7 402 " --> pdb=" O GLU 7 398 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER 7 407 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY 7 408 " --> pdb=" O LEU 7 404 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 420 removed outlier: 5.504A pdb=" N ALA 7 419 " --> pdb=" O ALA 7 415 " (cutoff:3.500A) Proline residue: 7 420 - end of helix Processing helix chain '7' and resid 425 through 438 removed outlier: 4.550A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU 7 435 " --> pdb=" O ALA 7 431 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU 7 436 " --> pdb=" O LEU 7 432 " (cutoff:3.500A) Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 511 through 517 removed outlier: 4.412A pdb=" N ASP 7 517 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 543 removed outlier: 3.877A pdb=" N ALA 7 536 " --> pdb=" O SER 7 532 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS 7 538 " --> pdb=" O ARG 7 534 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU 7 539 " --> pdb=" O THR 7 535 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL 7 540 " --> pdb=" O ALA 7 536 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 584 Processing helix chain '7' and resid 587 through 594 removed outlier: 5.195A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.656A pdb=" N HIS 7 615 " --> pdb=" O LYS 7 611 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET 7 621 " --> pdb=" O THR 7 617 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN 7 623 " --> pdb=" O VAL 7 619 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 649 removed outlier: 3.832A pdb=" N TYR 7 644 " --> pdb=" O GLU 7 640 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG 7 649 " --> pdb=" O ALA 7 645 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 673 removed outlier: 3.703A pdb=" N ASN 7 657 " --> pdb=" O SER 7 653 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL 7 661 " --> pdb=" O ASN 7 657 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN 7 662 " --> pdb=" O ASP 7 658 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG 7 666 " --> pdb=" O GLN 7 662 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG 7 673 " --> pdb=" O GLN 7 669 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.643A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 729 removed outlier: 4.311A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU 7 715 " --> pdb=" O ASP 7 711 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA 7 716 " --> pdb=" O ASP 7 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 24 removed outlier: 3.831A pdb=" N LYS A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 61 removed outlier: 3.776A pdb=" N GLN A 57 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 104 removed outlier: 3.911A pdb=" N LYS A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.506A pdb=" N LEU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 125 through 145 removed outlier: 4.359A pdb=" N GLY A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.768A pdb=" N VAL A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 removed outlier: 5.175A pdb=" N GLN B 9 " --> pdb=" O ALA B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.620A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 removed outlier: 4.637A pdb=" N LEU B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 63' Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.968A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 137 through 163 removed outlier: 4.003A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 201 removed outlier: 3.823A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.239A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.892A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.376A pdb=" N GLU C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 removed outlier: 4.579A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 removed outlier: 3.504A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.627A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.647A pdb=" N SER C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 140 removed outlier: 3.649A pdb=" N GLN C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 4.383A pdb=" N PHE C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 193 removed outlier: 4.037A pdb=" N GLU C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 removed outlier: 4.936A pdb=" N GLU D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.735A pdb=" N SER D 61 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 107 removed outlier: 3.531A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 155 Processing helix chain 'D' and resid 156 through 165 removed outlier: 5.363A pdb=" N GLU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 removed outlier: 3.683A pdb=" N LEU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 203 removed outlier: 3.547A pdb=" N LEU D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET D 202 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 278 through 289 removed outlier: 3.571A pdb=" N ILE D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 removed outlier: 3.574A pdb=" N ALA E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 53 Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 91 through 97 removed outlier: 3.606A pdb=" N GLU E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 removed outlier: 4.032A pdb=" N TYR E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 152 through 166 removed outlier: 4.664A pdb=" N ASP E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.036A pdb=" N GLN E 229 " --> pdb=" O GLN E 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 266 through 282 removed outlier: 4.279A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 303 removed outlier: 3.742A pdb=" N ARG E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) Proline residue: E 293 - end of helix removed outlier: 3.692A pdb=" N ASP E 297 " --> pdb=" O PRO E 293 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 341 removed outlier: 3.797A pdb=" N PHE E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER E 341 " --> pdb=" O SER E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 349 Processing helix chain 'E' and resid 352 through 367 Processing helix chain 'E' and resid 369 through 376 removed outlier: 4.066A pdb=" N GLU E 375 " --> pdb=" O SER E 371 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 395 removed outlier: 3.572A pdb=" N ARG E 386 " --> pdb=" O HIS E 382 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 434 Processing helix chain 'E' and resid 461 through 485 removed outlier: 3.891A pdb=" N LEU E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG E 472 " --> pdb=" O ASN E 468 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP E 485 " --> pdb=" O TRP E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 517 removed outlier: 3.748A pdb=" N GLN E 500 " --> pdb=" O ILE E 496 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG E 504 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA E 512 " --> pdb=" O ASN E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 560 removed outlier: 4.023A pdb=" N SER E 559 " --> pdb=" O CYS E 555 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU E 560 " --> pdb=" O CYS E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 617 removed outlier: 3.994A pdb=" N GLN E 610 " --> pdb=" O SER E 606 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP E 617 " --> pdb=" O THR E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 648 removed outlier: 3.501A pdb=" N LEU E 637 " --> pdb=" O ARG E 633 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix removed outlier: 4.167A pdb=" N LEU E 646 " --> pdb=" O GLU E 642 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY E 648 " --> pdb=" O LEU E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 removed outlier: 4.749A pdb=" N ARG E 406 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 540 removed outlier: 4.281A pdb=" N ARG E 540 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 681 removed outlier: 4.669A pdb=" N TYR F 676 " --> pdb=" O ALA F 672 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE F 679 " --> pdb=" O ASP F 675 " (cutoff:3.500A) Proline residue: F 681 - end of helix Processing helix chain 'F' and resid 723 through 733 removed outlier: 3.501A pdb=" N GLY F 733 " --> pdb=" O TRP F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 791 Processing helix chain 'F' and resid 818 through 844 Processing helix chain 'F' and resid 849 through 877 removed outlier: 4.513A pdb=" N GLU F 853 " --> pdb=" O GLY F 849 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER F 872 " --> pdb=" O ARG F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 890 removed outlier: 3.552A pdb=" N GLU F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 889 " --> pdb=" O LEU F 885 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS F 890 " --> pdb=" O ALA F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 906 removed outlier: 4.210A pdb=" N ALA F 897 " --> pdb=" O ARG F 893 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 898 " --> pdb=" O ALA F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 907 through 923 removed outlier: 3.600A pdb=" N VAL F 911 " --> pdb=" O LEU F 907 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F 919 " --> pdb=" O ASN F 915 " (cutoff:3.500A) Processing helix chain 'G' and resid 670 through 681 Proline residue: G 681 - end of helix Processing helix chain 'G' and resid 723 through 733 removed outlier: 3.651A pdb=" N GLU G 727 " --> pdb=" O ASP G 723 " (cutoff:3.500A) Processing helix chain 'G' and resid 782 through 790 Processing helix chain 'G' and resid 818 through 844 removed outlier: 3.577A pdb=" N GLU G 825 " --> pdb=" O MET G 821 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN G 843 " --> pdb=" O ASP G 839 " (cutoff:3.500A) Processing helix chain 'G' and resid 850 through 877 removed outlier: 3.687A pdb=" N ALA G 856 " --> pdb=" O ASN G 852 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 860 " --> pdb=" O ALA G 856 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 889 removed outlier: 3.604A pdb=" N LEU G 889 " --> pdb=" O LEU G 885 " (cutoff:3.500A) Processing helix chain 'G' and resid 891 through 906 removed outlier: 4.288A pdb=" N LEU G 895 " --> pdb=" O GLN G 891 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR G 896 " --> pdb=" O ASP G 892 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA G 897 " --> pdb=" O ARG G 893 " (cutoff:3.500A) Processing helix chain 'G' and resid 907 through 924 removed outlier: 4.082A pdb=" N VAL G 911 " --> pdb=" O LEU G 907 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN G 916 " --> pdb=" O LYS G 912 " (cutoff:3.500A) Processing helix chain 'H' and resid 670 through 681 removed outlier: 4.542A pdb=" N TYR H 676 " --> pdb=" O ALA H 672 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE H 679 " --> pdb=" O ASP H 675 " (cutoff:3.500A) Proline residue: H 681 - end of helix Processing helix chain 'H' and resid 723 through 733 removed outlier: 3.757A pdb=" N TRP H 729 " --> pdb=" O ASN H 725 " (cutoff:3.500A) Processing helix chain 'H' and resid 782 through 790 Processing helix chain 'H' and resid 818 through 843 removed outlier: 3.615A pdb=" N GLU H 825 " --> pdb=" O MET H 821 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN H 843 " --> pdb=" O ASP H 839 " (cutoff:3.500A) Processing helix chain 'H' and resid 850 through 877 Processing helix chain 'H' and resid 878 through 890 removed outlier: 6.256A pdb=" N LYS H 890 " --> pdb=" O ALA H 886 " (cutoff:3.500A) Processing helix chain 'H' and resid 891 through 906 removed outlier: 3.514A pdb=" N LEU H 895 " --> pdb=" O GLN H 891 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 899 " --> pdb=" O LEU H 895 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS H 900 " --> pdb=" O THR H 896 " (cutoff:3.500A) Processing helix chain 'H' and resid 907 through 924 removed outlier: 4.565A pdb=" N VAL H 911 " --> pdb=" O LEU H 907 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS H 912 " --> pdb=" O PRO H 908 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 33 removed outlier: 3.522A pdb=" N ILE X 31 " --> pdb=" O LEU X 27 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY X 33 " --> pdb=" O THR X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 66 Processing helix chain 'X' and resid 72 through 82 removed outlier: 4.118A pdb=" N ALA X 79 " --> pdb=" O ALA X 75 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU X 80 " --> pdb=" O MET X 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG X 82 " --> pdb=" O VAL X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 106 Proline residue: X 90 - end of helix removed outlier: 3.916A pdb=" N ALA X 102 " --> pdb=" O LYS X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 137 removed outlier: 4.163A pdb=" N LYS X 123 " --> pdb=" O ALA X 119 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE X 124 " --> pdb=" O TYR X 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 195 through 215 removed outlier: 4.007A pdb=" N VAL X 201 " --> pdb=" O ARG X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 249 removed outlier: 3.990A pdb=" N ILE X 248 " --> pdb=" O SER X 244 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER X 249 " --> pdb=" O MET X 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 244 through 249' Processing helix chain 'X' and resid 250 through 261 Processing helix chain 'X' and resid 262 through 273 removed outlier: 4.058A pdb=" N LEU X 273 " --> pdb=" O LEU X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 295 Processing helix chain 'X' and resid 299 through 304 removed outlier: 4.110A pdb=" N PHE X 303 " --> pdb=" O GLN X 299 " (cutoff:3.500A) Proline residue: X 304 - end of helix No H-bonds generated for 'chain 'X' and resid 299 through 304' Processing helix chain 'X' and resid 329 through 354 removed outlier: 5.351A pdb=" N SER X 354 " --> pdb=" O ILE X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 378 through 385 removed outlier: 3.789A pdb=" N LEU X 382 " --> pdb=" O GLY X 378 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL X 383 " --> pdb=" O SER X 379 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP X 384 " --> pdb=" O GLN X 380 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU X 385 " --> pdb=" O ALA X 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 378 through 385' Processing helix chain 'X' and resid 386 through 396 removed outlier: 4.345A pdb=" N LYS X 396 " --> pdb=" O LEU X 392 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 448 Processing helix chain 'X' and resid 449 through 464 removed outlier: 3.547A pdb=" N ASN X 458 " --> pdb=" O HIS X 454 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU X 463 " --> pdb=" O TYR X 459 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN X 464 " --> pdb=" O PHE X 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 468 through 493 removed outlier: 3.702A pdb=" N GLN X 472 " --> pdb=" O VAL X 468 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE X 478 " --> pdb=" O GLU X 474 " (cutoff:3.500A) Processing helix chain 'X' and resid 497 through 506 removed outlier: 5.010A pdb=" N VAL X 501 " --> pdb=" O ASP X 497 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER X 502 " --> pdb=" O ILE X 498 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU X 503 " --> pdb=" O LYS X 499 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA X 504 " --> pdb=" O GLN X 500 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU X 505 " --> pdb=" O VAL X 501 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS X 506 " --> pdb=" O SER X 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 497 through 506' Processing helix chain 'X' and resid 507 through 524 Processing helix chain 'X' and resid 525 through 550 Processing helix chain 'X' and resid 556 through 566 removed outlier: 5.131A pdb=" N SER X 566 " --> pdb=" O SER X 562 " (cutoff:3.500A) Processing helix chain 'X' and resid 567 through 584 Proline residue: X 577 - end of helix removed outlier: 4.197A pdb=" N SER X 581 " --> pdb=" O PRO X 577 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS X 582 " --> pdb=" O LYS X 578 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR X 583 " --> pdb=" O ILE X 579 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER X 584 " --> pdb=" O GLY X 580 " (cutoff:3.500A) Processing helix chain 'X' and resid 585 through 606 Processing helix chain 'X' and resid 658 through 668 removed outlier: 3.648A pdb=" N TYR X 666 " --> pdb=" O VAL X 662 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR X 668 " --> pdb=" O ALA X 664 " (cutoff:3.500A) Processing helix chain 'X' and resid 669 through 686 removed outlier: 3.920A pdb=" N ARG X 681 " --> pdb=" O ASN X 677 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE X 682 " --> pdb=" O PHE X 678 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG X 683 " --> pdb=" O LEU X 679 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU X 684 " --> pdb=" O GLU X 680 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU X 685 " --> pdb=" O ARG X 681 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU X 686 " --> pdb=" O PHE X 682 " (cutoff:3.500A) Processing helix chain 'X' and resid 687 through 702 Processing helix chain 'X' and resid 706 through 712 removed outlier: 4.594A pdb=" N LEU X 710 " --> pdb=" O GLU X 706 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG X 712 " --> pdb=" O ALA X 708 " (cutoff:3.500A) Processing helix chain 'X' and resid 713 through 724 Processing helix chain 'X' and resid 732 through 756 removed outlier: 3.804A pdb=" N LYS X 736 " --> pdb=" O SER X 732 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR X 737 " --> pdb=" O ARG X 733 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL X 738 " --> pdb=" O SER X 734 " (cutoff:3.500A) Processing helix chain 'X' and resid 758 through 766 removed outlier: 3.997A pdb=" N LEU X 764 " --> pdb=" O PHE X 760 " (cutoff:3.500A) Proline residue: X 766 - end of helix Processing helix chain 'X' and resid 771 through 780 Processing helix chain 'Y' and resid 55 through 60 Processing helix chain 'Y' and resid 64 through 76 removed outlier: 5.214A pdb=" N HIS Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 103 removed outlier: 3.900A pdb=" N PHE Y 94 " --> pdb=" O ASN Y 90 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR Y 95 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 122 Processing helix chain 'Y' and resid 123 through 139 Processing sheet with id= 1, first strand: chain '2' and resid 240 through 244 Processing sheet with id= 2, first strand: chain '2' and resid 317 through 322 Processing sheet with id= 3, first strand: chain '2' and resid 325 through 328 removed outlier: 3.519A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ARG 2 387 " --> pdb=" O THR 2 328 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG 2 404 " --> pdb=" O GLU 2 392 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '2' and resid 339 through 342 Processing sheet with id= 5, first strand: chain '2' and resid 562 through 567 removed outlier: 4.787A pdb=" N ARG 2 562 " --> pdb=" O LYS 2 601 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY 2 602 " --> pdb=" O ARG 2 643 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE 2 537 " --> pdb=" O CYS 2 644 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE 2 646 " --> pdb=" O ILE 2 537 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '2' and resid 579 through 583 removed outlier: 6.829A pdb=" N SER 2 579 " --> pdb=" O LEU 2 591 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU 2 591 " --> pdb=" O SER 2 579 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG 2 581 " --> pdb=" O TRP 2 589 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP 2 589 " --> pdb=" O ARG 2 581 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP 2 583 " --> pdb=" O LYS 2 587 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '3' and resid 94 through 98 Processing sheet with id= 8, first strand: chain '3' and resid 179 through 184 Processing sheet with id= 9, first strand: chain '3' and resid 207 through 213 removed outlier: 3.855A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL 3 200 " --> pdb=" O GLU 3 244 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '3' and resid 253 through 260 removed outlier: 5.618A pdb=" N ARG 3 272 " --> pdb=" O GLU 3 260 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP 3 279 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '3' and resid 428 through 433 removed outlier: 5.759A pdb=" N LEU 3 428 " --> pdb=" O ARG 3 467 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY 3 468 " --> pdb=" O ARG 3 509 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE 3 403 " --> pdb=" O CYS 3 510 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL 3 512 " --> pdb=" O ILE 3 403 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '3' and resid 445 through 448 Processing sheet with id= 13, first strand: chain '4' and resid 239 through 243 Processing sheet with id= 14, first strand: chain '4' and resid 325 through 330 Processing sheet with id= 15, first strand: chain '4' and resid 333 through 336 removed outlier: 3.736A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL 4 396 " --> pdb=" O THR 4 336 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '4' and resid 354 through 359 removed outlier: 4.516A pdb=" N HIS 4 354 " --> pdb=" O CYS 4 349 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N SER 4 381 " --> pdb=" O ASN 4 350 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '4' and resid 460 through 463 Processing sheet with id= 18, first strand: chain '4' and resid 587 through 592 removed outlier: 5.727A pdb=" N VAL 4 628 " --> pdb=" O ARG 4 587 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER 4 670 " --> pdb=" O GLY 4 627 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE 4 562 " --> pdb=" O SER 4 669 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 562 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '4' and resid 915 through 920 removed outlier: 8.189A pdb=" N LYS 4 915 " --> pdb=" O VAL 4 927 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '4' and resid 393 through 401 removed outlier: 5.838A pdb=" N ASP 4 393 " --> pdb=" O ASP 4 421 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS 4 413 " --> pdb=" O GLU 4 401 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '4' and resid 652 through 657 removed outlier: 7.733A pdb=" N GLN 4 652 " --> pdb=" O ALA 4 667 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '5' and resid 59 through 63 Processing sheet with id= 23, first strand: chain '5' and resid 159 through 164 Processing sheet with id= 24, first strand: chain '5' and resid 172 through 177 removed outlier: 5.953A pdb=" N ARG 5 272 " --> pdb=" O GLU 5 260 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '5' and resid 188 through 193 removed outlier: 4.697A pdb=" N HIS 5 188 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '5' and resid 435 through 439 removed outlier: 5.567A pdb=" N ILE 5 435 " --> pdb=" O GLY 5 474 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY 5 475 " --> pdb=" O ARG 5 516 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE 5 410 " --> pdb=" O THR 5 517 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL 5 519 " --> pdb=" O ILE 5 410 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '5' and resid 451 through 457 removed outlier: 3.994A pdb=" N GLU 5 461 " --> pdb=" O ASP 5 456 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '6' and resid 123 through 126 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain '6' and resid 149 through 153 Processing sheet with id= 30, first strand: chain '6' and resid 288 through 293 removed outlier: 5.849A pdb=" N ARG 6 394 " --> pdb=" O ILE 6 462 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '6' and resid 295 through 298 removed outlier: 5.549A pdb=" N LYS 6 358 " --> pdb=" O SER 6 298 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '6' and resid 315 through 319 removed outlier: 4.276A pdb=" N ALA 6 316 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER 6 308 " --> pdb=" O ASN 6 347 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '6' and resid 400 through 405 Processing sheet with id= 34, first strand: chain '6' and resid 594 through 599 removed outlier: 5.908A pdb=" N ARG 6 594 " --> pdb=" O ASN 6 633 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE 6 635 " --> pdb=" O ARG 6 594 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY 6 634 " --> pdb=" O ARG 6 675 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE 6 569 " --> pdb=" O THR 6 676 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE 6 678 " --> pdb=" O ILE 6 569 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU 6 711 " --> pdb=" O ASN 6 570 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '6' and resid 610 through 614 Processing sheet with id= 36, first strand: chain '6' and resid 356 through 363 removed outlier: 5.750A pdb=" N ARG 6 375 " --> pdb=" O GLU 6 363 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '6' and resid 659 through 664 removed outlier: 4.742A pdb=" N GLN 6 659 " --> pdb=" O ALA 6 674 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '7' and resid 76 through 80 Processing sheet with id= 39, first strand: chain '7' and resid 238 through 243 Processing sheet with id= 40, first strand: chain '7' and resid 246 through 249 removed outlier: 3.660A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU 7 312 " --> pdb=" O SER 7 249 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '7' and resid 266 through 272 removed outlier: 3.839A pdb=" N TYR 7 267 " --> pdb=" O CYS 7 262 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN 7 297 " --> pdb=" O ASP 7 263 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '7' and resid 375 through 378 Processing sheet with id= 43, first strand: chain '7' and resid 440 through 443 removed outlier: 3.804A pdb=" N VAL 7 440 " --> pdb=" O GLY 7 452 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY 7 452 " --> pdb=" O VAL 7 440 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '7' and resid 479 through 484 removed outlier: 5.980A pdb=" N ARG 7 479 " --> pdb=" O ASN 7 518 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE 7 520 " --> pdb=" O ARG 7 479 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY 7 519 " --> pdb=" O ARG 7 560 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE 7 454 " --> pdb=" O THR 7 561 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE 7 563 " --> pdb=" O ILE 7 454 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP 7 461 " --> pdb=" O MET 7 600 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '7' and resid 309 through 316 removed outlier: 5.430A pdb=" N ALA 7 309 " --> pdb=" O GLY 7 337 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'A' and resid 187 through 191 removed outlier: 4.712A pdb=" N SER A 187 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N TYR A 204 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'D' and resid 246 through 249 removed outlier: 4.274A pdb=" N LYS D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 273 through 277 removed outlier: 4.321A pdb=" N SER D 273 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHE D 229 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'E' and resid 56 through 62 removed outlier: 3.578A pdb=" N SER E 80 " --> pdb=" O GLN E 26 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 139 " --> pdb=" O ARG E 118 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'E' and resid 317 through 322 Processing sheet with id= 51, first strand: chain 'E' and resid 525 through 530 removed outlier: 7.348A pdb=" N LEU E 565 " --> pdb=" O PRO E 586 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR E 578 " --> pdb=" O ASP E 573 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N SER E 628 " --> pdb=" O GLY E 583 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 483 through 486 removed outlier: 4.484A pdb=" N TYR F 493 " --> pdb=" O THR F 484 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE F 486 " --> pdb=" O ARG F 491 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG F 491 " --> pdb=" O PHE F 486 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP F 490 " --> pdb=" O LYS F 506 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL F 502 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL F 499 " --> pdb=" O PHE F 518 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN F 510 " --> pdb=" O ASN F 507 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'F' and resid 536 through 540 removed outlier: 3.850A pdb=" N GLY F 543 " --> pdb=" O ASN F 540 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LYS F 542 " --> pdb=" O HIS F 559 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 553 " --> pdb=" O GLN F 548 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY F 552 " --> pdb=" O ILE F 570 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'F' and resid 580 through 584 removed outlier: 4.241A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY F 595 " --> pdb=" O THR F 612 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'F' and resid 617 through 621 removed outlier: 8.022A pdb=" N TYR F 623 " --> pdb=" O LEU F 643 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER F 631 " --> pdb=" O GLY F 635 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU F 640 " --> pdb=" O TYR F 651 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'F' and resid 686 through 689 removed outlier: 3.628A pdb=" N SER F 686 " --> pdb=" O PHE F 698 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU F 704 " --> pdb=" O ILE F 721 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'F' and resid 739 through 745 removed outlier: 5.353A pdb=" N ASP F 739 " --> pdb=" O GLY F 759 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN F 753 " --> pdb=" O LEU F 745 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'F' and resid 636 through 639 removed outlier: 6.128A pdb=" N LEU F 636 " --> pdb=" O LEU F 657 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'G' and resid 490 through 494 removed outlier: 6.784A pdb=" N ASP G 490 " --> pdb=" O LYS G 506 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL G 502 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR G 501 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR G 526 " --> pdb=" O VAL G 515 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 535 through 540 removed outlier: 3.666A pdb=" N GLY G 543 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LYS G 542 " --> pdb=" O HIS G 559 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN G 553 " --> pdb=" O GLN G 548 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY G 552 " --> pdb=" O ILE G 570 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'G' and resid 580 through 584 removed outlier: 4.274A pdb=" N SER G 580 " --> pdb=" O GLY G 591 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL G 588 " --> pdb=" O SER G 599 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER G 599 " --> pdb=" O VAL G 588 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 590 " --> pdb=" O PHE G 597 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE G 597 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR G 592 " --> pdb=" O GLY G 595 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY G 595 " --> pdb=" O THR G 612 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA G 608 " --> pdb=" O SER G 599 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'G' and resid 623 through 631 removed outlier: 6.897A pdb=" N TYR G 623 " --> pdb=" O LEU G 643 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER G 631 " --> pdb=" O GLY G 635 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU G 640 " --> pdb=" O TYR G 651 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'G' and resid 685 through 689 removed outlier: 3.512A pdb=" N SER G 686 " --> pdb=" O PHE G 698 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU G 704 " --> pdb=" O ILE G 721 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'G' and resid 739 through 745 removed outlier: 4.825A pdb=" N ASP G 739 " --> pdb=" O GLY G 759 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY G 759 " --> pdb=" O ASP G 739 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN G 753 " --> pdb=" O LEU G 745 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'H' and resid 490 through 494 removed outlier: 7.591A pdb=" N ASP H 490 " --> pdb=" O LYS H 506 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 502 " --> pdb=" O LEU H 494 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'H' and resid 535 through 541 removed outlier: 3.588A pdb=" N GLY H 543 " --> pdb=" O ASN H 540 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LYS H 542 " --> pdb=" O HIS H 559 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN H 553 " --> pdb=" O GLN H 548 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY H 552 " --> pdb=" O ILE H 570 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'H' and resid 580 through 584 removed outlier: 3.657A pdb=" N ARG H 587 " --> pdb=" O THR H 584 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 588 " --> pdb=" O SER H 599 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER H 599 " --> pdb=" O VAL H 588 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL H 590 " --> pdb=" O PHE H 597 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE H 597 " --> pdb=" O VAL H 590 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR H 592 " --> pdb=" O GLY H 595 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY H 595 " --> pdb=" O THR H 612 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'H' and resid 617 through 621 removed outlier: 6.654A pdb=" N TYR H 623 " --> pdb=" O LEU H 643 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER H 631 " --> pdb=" O GLY H 635 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU H 640 " --> pdb=" O TYR H 651 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER H 647 " --> pdb=" O GLY H 644 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'H' and resid 686 through 689 removed outlier: 3.574A pdb=" N SER H 686 " --> pdb=" O PHE H 698 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU H 704 " --> pdb=" O ILE H 721 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'H' and resid 739 through 745 removed outlier: 4.570A pdb=" N ASP H 739 " --> pdb=" O GLY H 759 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN H 753 " --> pdb=" O LEU H 745 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 363 through 368 2783 hydrogen bonds defined for protein. 8229 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: 40.85 Time building geometry restraints manager: 73.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 58905 1.12 - 1.29: 10289 1.29 - 1.47: 21594 1.47 - 1.64: 28164 1.64 - 1.82: 414 Bond restraints: 119366 Sorted by residual: bond pdb=" N3B ANP 5 801 " pdb=" PG ANP 5 801 " ideal model delta sigma weight residual 1.795 1.574 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" N3B ANP 31500 " pdb=" PG ANP 31500 " ideal model delta sigma weight residual 1.795 1.584 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" N3B ANP 2 902 " pdb=" PG ANP 2 902 " ideal model delta sigma weight residual 1.795 1.599 0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" O3A ANP 31500 " pdb=" PB ANP 31500 " ideal model delta sigma weight residual 1.700 1.534 0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" O3A ANP 2 902 " pdb=" PB ANP 2 902 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.24e+01 ... (remaining 119361 not shown) Histogram of bond angle deviations from ideal: 93.38 - 101.85: 252 101.85 - 110.33: 118335 110.33 - 118.81: 47987 118.81 - 127.28: 48678 127.28 - 135.76: 725 Bond angle restraints: 215977 Sorted by residual: angle pdb=" C LYS 2 587 " pdb=" CA LYS 2 587 " pdb=" CB LYS 2 587 " ideal model delta sigma weight residual 111.86 123.42 -11.56 1.34e+00 5.57e-01 7.44e+01 angle pdb=" N ASP B 171 " pdb=" CA ASP B 171 " pdb=" C ASP B 171 " ideal model delta sigma weight residual 111.11 120.55 -9.44 1.20e+00 6.94e-01 6.19e+01 angle pdb=" C6 DA I 38 " pdb=" N6 DA I 38 " pdb=" H61 DA I 38 " ideal model delta sigma weight residual 120.00 108.22 11.78 1.50e+00 4.44e-01 6.17e+01 angle pdb=" CA ASP 5 41 " pdb=" CB ASP 5 41 " pdb=" CG ASP 5 41 " ideal model delta sigma weight residual 112.60 120.26 -7.66 1.00e+00 1.00e+00 5.87e+01 angle pdb=" N LEU C 169 " pdb=" CA LEU C 169 " pdb=" C LEU C 169 " ideal model delta sigma weight residual 109.07 120.15 -11.08 1.61e+00 3.86e-01 4.74e+01 ... (remaining 215972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.42: 52347 30.42 - 60.84: 2219 60.84 - 91.26: 511 91.26 - 121.68: 0 121.68 - 152.10: 3 Dihedral angle restraints: 55080 sinusoidal: 30459 harmonic: 24621 Sorted by residual: dihedral pdb=" C PHE H 603 " pdb=" N PHE H 603 " pdb=" CA PHE H 603 " pdb=" CB PHE H 603 " ideal model delta harmonic sigma weight residual -122.60 -142.00 19.40 0 2.50e+00 1.60e-01 6.02e+01 dihedral pdb=" C VAL H 588 " pdb=" N VAL H 588 " pdb=" CA VAL H 588 " pdb=" CB VAL H 588 " ideal model delta harmonic sigma weight residual -122.00 -141.12 19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C LEU C 169 " pdb=" N LEU C 169 " pdb=" CA LEU C 169 " pdb=" CB LEU C 169 " ideal model delta harmonic sigma weight residual -122.60 -141.61 19.01 0 2.50e+00 1.60e-01 5.78e+01 ... (remaining 55077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 7996 0.145 - 0.290: 1195 0.290 - 0.434: 129 0.434 - 0.579: 16 0.579 - 0.724: 7 Chirality restraints: 9343 Sorted by residual: chirality pdb=" CA LEU C 169 " pdb=" N LEU C 169 " pdb=" C LEU C 169 " pdb=" CB LEU C 169 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA PHE H 603 " pdb=" N PHE H 603 " pdb=" C PHE H 603 " pdb=" CB PHE H 603 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA VAL H 588 " pdb=" N VAL H 588 " pdb=" C VAL H 588 " pdb=" CB VAL H 588 " both_signs ideal model delta sigma weight residual False 2.44 1.79 0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 9340 not shown) Planarity restraints: 17180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 58 " 0.324 2.00e-02 2.50e+03 1.45e-01 6.34e+02 pdb=" N1 DT I 58 " -0.006 2.00e-02 2.50e+03 pdb=" C2 DT I 58 " -0.064 2.00e-02 2.50e+03 pdb=" O2 DT I 58 " -0.063 2.00e-02 2.50e+03 pdb=" N3 DT I 58 " -0.056 2.00e-02 2.50e+03 pdb=" C4 DT I 58 " 0.085 2.00e-02 2.50e+03 pdb=" O4 DT I 58 " 0.239 2.00e-02 2.50e+03 pdb=" C5 DT I 58 " -0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 58 " -0.013 2.00e-02 2.50e+03 pdb=" C6 DT I 58 " -0.080 2.00e-02 2.50e+03 pdb=" H3 DT I 58 " -0.163 2.00e-02 2.50e+03 pdb=" H6 DT I 58 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 5 343 " 0.226 2.00e-02 2.50e+03 1.07e-01 4.61e+02 pdb=" CG TRP 5 343 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP 5 343 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP 5 343 " -0.090 2.00e-02 2.50e+03 pdb=" NE1 TRP 5 343 " -0.099 2.00e-02 2.50e+03 pdb=" CE2 TRP 5 343 " -0.045 2.00e-02 2.50e+03 pdb=" CE3 TRP 5 343 " -0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP 5 343 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP 5 343 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP 5 343 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 TRP 5 343 " 0.106 2.00e-02 2.50e+03 pdb=" HE1 TRP 5 343 " -0.208 2.00e-02 2.50e+03 pdb=" HE3 TRP 5 343 " -0.118 2.00e-02 2.50e+03 pdb=" HZ2 TRP 5 343 " 0.137 2.00e-02 2.50e+03 pdb=" HZ3 TRP 5 343 " -0.031 2.00e-02 2.50e+03 pdb=" HH2 TRP 5 343 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 55 " 0.289 2.00e-02 2.50e+03 1.15e-01 3.94e+02 pdb=" N1 DT I 55 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 55 " -0.058 2.00e-02 2.50e+03 pdb=" O2 DT I 55 " -0.064 2.00e-02 2.50e+03 pdb=" N3 DT I 55 " -0.031 2.00e-02 2.50e+03 pdb=" C4 DT I 55 " 0.047 2.00e-02 2.50e+03 pdb=" O4 DT I 55 " 0.149 2.00e-02 2.50e+03 pdb=" C5 DT I 55 " -0.013 2.00e-02 2.50e+03 pdb=" C7 DT I 55 " 0.035 2.00e-02 2.50e+03 pdb=" C6 DT I 55 " -0.078 2.00e-02 2.50e+03 pdb=" H3 DT I 55 " -0.073 2.00e-02 2.50e+03 pdb=" H6 DT I 55 " -0.165 2.00e-02 2.50e+03 ... (remaining 17177 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 4350 2.08 - 2.71: 174280 2.71 - 3.34: 345983 3.34 - 3.97: 457087 3.97 - 4.60: 678051 Nonbonded interactions: 1659751 Sorted by model distance: nonbonded pdb=" HG SER H 480 " pdb=" H CYS H 537 " model vdw 1.453 2.100 nonbonded pdb=" HZ3 LYS A 142 " pdb=" HG SER A 152 " model vdw 1.537 2.100 nonbonded pdb=" HG1 THR B 10 " pdb=" H PHE B 11 " model vdw 1.546 2.100 nonbonded pdb=" H GLN X 707 " pdb=" HG3 GLN X 707 " model vdw 1.555 2.270 nonbonded pdb=" HG2 GLU H 765 " pdb=" H PHE H 766 " model vdw 1.572 2.270 ... (remaining 1659746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and (resid 474 through 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 814 through 892 or (resid 893 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 894 through 901 or (resid 902 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 90 \ 3 through 911 or (resid 912 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 814 through 901 or (r \ esid 902 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 903 through 909 or (resid 910 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 911 through 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 894 through 909 or (resid 910 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 911 or (resid 912 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 913 through 92 \ 3)) } 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.250 Extract box with map and model: 13.660 Check model and map are aligned: 1.270 Set scattering table: 0.770 Process input model: 329.450 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.310 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 355.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.013 0.221 60369 Z= 0.821 Angle : 1.931 20.304 81868 Z= 1.290 Chirality : 0.107 0.724 9343 Planarity : 0.017 0.228 10259 Dihedral : 15.512 152.096 22958 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.53 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.09), residues: 7117 helix: -1.53 (0.08), residues: 3086 sheet: -0.23 (0.15), residues: 1025 loop : -0.76 (0.11), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.158 0.022 TRP 5 343 HIS 0.018 0.004 HIS 3 712 PHE 0.116 0.013 PHE 2 271 TYR 0.214 0.024 TYR E 233 ARG 0.019 0.002 ARG 5 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 1444 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1438 time to evaluate : 6.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 365 ILE cc_start: 0.9463 (mt) cc_final: 0.9203 (mt) REVERT: 4 881 MET cc_start: 0.3466 (ttm) cc_final: 0.2926 (ttm) REVERT: 5 458 MET cc_start: 0.7371 (mtm) cc_final: 0.6880 (tpt) REVERT: 6 332 PHE cc_start: 0.6940 (m-80) cc_final: 0.6608 (m-80) REVERT: 7 457 CYS cc_start: 0.6397 (t) cc_final: 0.5952 (t) REVERT: 7 497 VAL cc_start: 0.7363 (t) cc_final: 0.7139 (m) REVERT: 7 529 MET cc_start: 0.6845 (ttm) cc_final: 0.6623 (ttp) REVERT: 7 608 ASP cc_start: 0.8730 (m-30) cc_final: 0.8019 (t0) REVERT: 7 667 LEU cc_start: 0.7357 (mt) cc_final: 0.7136 (mm) REVERT: A 23 SER cc_start: 0.5371 (t) cc_final: 0.5114 (p) REVERT: C -2 MET cc_start: 0.6634 (ptm) cc_final: 0.5823 (tpt) REVERT: C 1 MET cc_start: 0.5287 (ptp) cc_final: 0.4921 (ptp) REVERT: C 3 TYR cc_start: 0.8500 (t80) cc_final: 0.7943 (t80) REVERT: C 29 TYR cc_start: 0.8119 (p90) cc_final: 0.7604 (p90) REVERT: E 245 THR cc_start: 0.8317 (m) cc_final: 0.7995 (p) REVERT: E 543 LEU cc_start: 0.9136 (mt) cc_final: 0.8868 (mt) REVERT: E 622 ILE cc_start: 0.7696 (tp) cc_final: 0.7356 (tt) REVERT: H 869 LEU cc_start: 0.8111 (mt) cc_final: 0.7855 (mt) REVERT: X 233 ILE cc_start: 0.7788 (mp) cc_final: 0.7584 (mp) REVERT: X 345 MET cc_start: 0.8417 (mmm) cc_final: 0.7978 (tmm) REVERT: X 456 VAL cc_start: 0.8684 (m) cc_final: 0.8466 (m) REVERT: X 484 LYS cc_start: 0.9081 (tttt) cc_final: 0.8728 (tppt) REVERT: X 537 ASN cc_start: 0.8517 (t0) cc_final: 0.8125 (t0) REVERT: X 673 GLU cc_start: 0.8209 (tp30) cc_final: 0.7946 (tp30) REVERT: X 718 LEU cc_start: 0.9472 (tp) cc_final: 0.9064 (tp) outliers start: 6 outliers final: 2 residues processed: 1443 average time/residue: 1.5526 time to fit residues: 3608.6552 Evaluate side-chains 777 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 775 time to evaluate : 6.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 442 LYS Chi-restraints excluded: chain H residue 837 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 609 optimal weight: 6.9990 chunk 547 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 369 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 chunk 565 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 421 optimal weight: 5.9990 chunk 655 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 391 GLN 2 531 HIS 2 627 GLN 2 760 GLN 3 51 ASN 4 307 ASN 4 400 GLN 4 759 HIS 5 52 ASN 5 58 ASN 5 140 ASN 5 359 GLN 5 372 ASN 5 524 ASN ** 5 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 362 GLN 6 570 ASN 7 124 ASN 7 316 GLN 7 543 GLN 7 683 GLN A 193 GLN B 62 ASN B 167 HIS C 86 ASN E 130 ASN E 254 GLN E 508 ASN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 678 ASN ** F 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 527 HIS G 634 HIS ** G 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 915 ASN X 537 ASN X 665 ASN Y 96 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 60369 Z= 0.400 Angle : 0.760 8.165 81868 Z= 0.414 Chirality : 0.043 0.215 9343 Planarity : 0.006 0.077 10259 Dihedral : 12.266 158.924 8626 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 1.77 % Allowed : 8.44 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 7117 helix: -0.02 (0.09), residues: 3134 sheet: -0.56 (0.14), residues: 1208 loop : -0.67 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 729 HIS 0.010 0.002 HIS 6 669 PHE 0.028 0.002 PHE X 293 TYR 0.020 0.002 TYR H 922 ARG 0.008 0.001 ARG 4 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 855 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 741 time to evaluate : 6.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 818 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: 5 465 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6210 (mm-30) REVERT: 6 332 PHE cc_start: 0.7116 (m-80) cc_final: 0.6908 (m-10) REVERT: 7 457 CYS cc_start: 0.6707 (t) cc_final: 0.6367 (t) REVERT: 7 497 VAL cc_start: 0.7572 (t) cc_final: 0.7354 (m) REVERT: 7 529 MET cc_start: 0.7230 (ttm) cc_final: 0.7019 (mtp) REVERT: 7 571 TYR cc_start: 0.6327 (m-80) cc_final: 0.5488 (m-80) REVERT: A 160 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: E 245 THR cc_start: 0.8392 (m) cc_final: 0.8028 (p) REVERT: X 296 ASP cc_start: 0.8180 (p0) cc_final: 0.7949 (p0) REVERT: X 345 MET cc_start: 0.8382 (mmm) cc_final: 0.8038 (tmm) outliers start: 114 outliers final: 74 residues processed: 818 average time/residue: 1.4069 time to fit residues: 1882.2934 Evaluate side-chains 635 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 558 time to evaluate : 6.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 587 LYS Chi-restraints excluded: chain 2 residue 596 LEU Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 701 ASP Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 284 ASP Chi-restraints excluded: chain 3 residue 358 ASP Chi-restraints excluded: chain 3 residue 375 ASP Chi-restraints excluded: chain 3 residue 407 MET Chi-restraints excluded: chain 3 residue 583 ARG Chi-restraints excluded: chain 3 residue 732 LEU Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 381 SER Chi-restraints excluded: chain 4 residue 561 ASP Chi-restraints excluded: chain 4 residue 575 SER Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 644 VAL Chi-restraints excluded: chain 4 residue 704 LEU Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 5 residue 41 ASP Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 435 ILE Chi-restraints excluded: chain 5 residue 465 GLU Chi-restraints excluded: chain 5 residue 629 ILE Chi-restraints excluded: chain 5 residue 662 SER Chi-restraints excluded: chain 6 residue 306 LYS Chi-restraints excluded: chain 6 residue 393 ASP Chi-restraints excluded: chain 6 residue 533 ILE Chi-restraints excluded: chain 6 residue 620 ASP Chi-restraints excluded: chain 6 residue 679 LEU Chi-restraints excluded: chain 6 residue 727 LEU Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 7 residue 339 LEU Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 616 VAL Chi-restraints excluded: chain 7 residue 617 THR Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 561 SER Chi-restraints excluded: chain F residue 697 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 752 LEU Chi-restraints excluded: chain G residue 785 LYS Chi-restraints excluded: chain G residue 837 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 646 SER Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 187 ILE Chi-restraints excluded: chain X residue 284 ILE Chi-restraints excluded: chain X residue 349 VAL Chi-restraints excluded: chain X residue 593 GLU Chi-restraints excluded: chain X residue 702 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Y residue 135 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 364 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 545 optimal weight: 3.9990 chunk 446 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 656 optimal weight: 10.0000 chunk 709 optimal weight: 9.9990 chunk 584 optimal weight: 20.0000 chunk 651 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 526 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 52 ASN 4 247 ASN 4 327 ASN 4 911 GLN 5 372 ASN ** 5 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 264 GLN 7 274 ASN D 249 ASN E 296 GLN E 395 ASN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 573 GLN H 553 GLN X 258 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 60369 Z= 0.322 Angle : 0.642 11.882 81868 Z= 0.353 Chirality : 0.043 0.192 9343 Planarity : 0.005 0.087 10259 Dihedral : 11.497 157.313 8620 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.64 % Favored : 96.35 % Rotamer: Outliers : 1.78 % Allowed : 9.83 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 7117 helix: 0.55 (0.09), residues: 3159 sheet: -0.61 (0.14), residues: 1201 loop : -0.60 (0.12), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 5 343 HIS 0.007 0.001 HIS H 527 PHE 0.023 0.002 PHE X 293 TYR 0.027 0.002 TYR 4 558 ARG 0.010 0.001 ARG 6 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 708 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 593 time to evaluate : 6.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 809 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5945 (t-90) REVERT: 4 644 VAL cc_start: 0.4928 (t) cc_final: 0.4102 (p) REVERT: 4 818 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: 5 465 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6210 (mm-30) REVERT: 7 497 VAL cc_start: 0.7604 (t) cc_final: 0.7399 (m) REVERT: 7 529 MET cc_start: 0.7504 (ttm) cc_final: 0.7160 (ttp) REVERT: 7 717 LEU cc_start: 0.8795 (tt) cc_final: 0.8542 (tp) REVERT: A 62 MET cc_start: 0.5563 (ppp) cc_final: 0.5324 (ppp) REVERT: B 66 MET cc_start: 0.8482 (mmt) cc_final: 0.8259 (mmm) REVERT: C 3 TYR cc_start: 0.8672 (t80) cc_final: 0.8205 (t80) REVERT: X 345 MET cc_start: 0.8391 (mmm) cc_final: 0.7904 (tmm) REVERT: X 593 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8226 (mt-10) outliers start: 115 outliers final: 79 residues processed: 677 average time/residue: 1.3334 time to fit residues: 1499.3077 Evaluate side-chains 589 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 506 time to evaluate : 6.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 587 LYS Chi-restraints excluded: chain 2 residue 596 LEU Chi-restraints excluded: chain 2 residue 646 ILE Chi-restraints excluded: chain 2 residue 701 ASP Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 809 HIS Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 284 ASP Chi-restraints excluded: chain 3 residue 402 ASP Chi-restraints excluded: chain 4 residue 217 ASN Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 724 LEU Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 5 residue 41 ASP Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 368 GLU Chi-restraints excluded: chain 5 residue 372 ASN Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 465 GLU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 6 residue 306 LYS Chi-restraints excluded: chain 6 residue 393 ASP Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 516 LEU Chi-restraints excluded: chain 6 residue 533 ILE Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 736 MET Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 289 CYS Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 573 ASP Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 774 MET Chi-restraints excluded: chain G residue 495 THR Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 785 LYS Chi-restraints excluded: chain G residue 827 TYR Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 592 THR Chi-restraints excluded: chain H residue 646 SER Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain H residue 906 GLU Chi-restraints excluded: chain H residue 922 TYR Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 187 ILE Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 284 ILE Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain X residue 593 GLU Chi-restraints excluded: chain X residue 699 ARG Chi-restraints excluded: chain X residue 702 VAL Chi-restraints excluded: chain Y residue 135 ASP Chi-restraints excluded: chain Y residue 139 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 648 optimal weight: 8.9990 chunk 493 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 313 optimal weight: 20.0000 chunk 441 optimal weight: 8.9990 chunk 659 optimal weight: 9.9990 chunk 697 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 624 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 201 HIS ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 305 ASN ** 5 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 570 ASN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 657 ASN A 33 HIS A 57 GLN D 249 ASN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN ** F 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 621 GLN G 622 ASN ** G 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 553 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 60369 Z= 0.373 Angle : 0.639 8.946 81868 Z= 0.351 Chirality : 0.042 0.213 9343 Planarity : 0.005 0.063 10259 Dihedral : 11.293 158.327 8620 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 11.20 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.10), residues: 7117 helix: 0.66 (0.09), residues: 3164 sheet: -0.76 (0.14), residues: 1225 loop : -0.72 (0.12), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 729 HIS 0.012 0.001 HIS E 22 PHE 0.026 0.002 PHE 2 609 TYR 0.018 0.002 TYR H 862 ARG 0.008 0.001 ARG Y 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 660 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 517 time to evaluate : 7.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 416 ASP cc_start: 0.7575 (t0) cc_final: 0.7248 (t0) REVERT: 2 809 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.5988 (t-90) REVERT: 4 314 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7589 (tmm) REVERT: 4 561 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5569 (t70) REVERT: 4 644 VAL cc_start: 0.5364 (t) cc_final: 0.4618 (p) REVERT: 5 465 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: 5 689 MET cc_start: 0.7251 (mmm) cc_final: 0.6684 (mmm) REVERT: 7 529 MET cc_start: 0.7689 (ttm) cc_final: 0.7104 (ttp) REVERT: 7 717 LEU cc_start: 0.8773 (tt) cc_final: 0.8531 (tp) REVERT: A 62 MET cc_start: 0.5541 (ppp) cc_final: 0.5192 (ppp) REVERT: C 170 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6079 (mt-10) REVERT: E 617 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.5923 (t0) REVERT: G 629 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.5569 (m-70) REVERT: G 707 LEU cc_start: 0.7780 (tp) cc_final: 0.7513 (tp) REVERT: H 570 ILE cc_start: 0.7182 (mm) cc_final: 0.6905 (mm) REVERT: X 345 MET cc_start: 0.8461 (mmm) cc_final: 0.7945 (tmm) REVERT: X 437 PHE cc_start: 0.8463 (t80) cc_final: 0.8229 (t80) outliers start: 143 outliers final: 100 residues processed: 626 average time/residue: 1.3905 time to fit residues: 1470.7630 Evaluate side-chains 575 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 469 time to evaluate : 6.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 361 ILE Chi-restraints excluded: chain 2 residue 596 LEU Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 701 ASP Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 809 HIS Chi-restraints excluded: chain 2 residue 843 ASP Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 284 ASP Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 478 MET Chi-restraints excluded: chain 4 residue 217 ASN Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 561 ASP Chi-restraints excluded: chain 4 residue 575 SER Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 641 THR Chi-restraints excluded: chain 4 residue 704 LEU Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 5 residue 41 ASP Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 465 GLU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 559 ASP Chi-restraints excluded: chain 5 residue 637 GLU Chi-restraints excluded: chain 6 residue 147 ASP Chi-restraints excluded: chain 6 residue 393 ASP Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 533 ILE Chi-restraints excluded: chain 6 residue 548 LEU Chi-restraints excluded: chain 6 residue 736 MET Chi-restraints excluded: chain 6 residue 801 GLU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 20 GLU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 289 CYS Chi-restraints excluded: chain 7 residue 459 MET Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 571 TYR Chi-restraints excluded: chain 7 residue 608 ASP Chi-restraints excluded: chain 7 residue 617 THR Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 617 ASP Chi-restraints excluded: chain F residue 510 GLN Chi-restraints excluded: chain F residue 774 MET Chi-restraints excluded: chain G residue 495 THR Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 690 SER Chi-restraints excluded: chain G residue 696 CYS Chi-restraints excluded: chain G residue 752 LEU Chi-restraints excluded: chain G residue 785 LYS Chi-restraints excluded: chain G residue 827 TYR Chi-restraints excluded: chain G residue 837 LEU Chi-restraints excluded: chain G residue 848 TYR Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 554 ILE Chi-restraints excluded: chain H residue 592 THR Chi-restraints excluded: chain H residue 646 SER Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain H residue 906 GLU Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain X residue 187 ILE Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 284 ILE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain X residue 593 GLU Chi-restraints excluded: chain X residue 699 ARG Chi-restraints excluded: chain X residue 702 VAL Chi-restraints excluded: chain X residue 763 LEU Chi-restraints excluded: chain Y residue 135 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 581 optimal weight: 10.0000 chunk 396 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 519 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 595 optimal weight: 20.0000 chunk 482 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 626 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 217 ASN ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 210 ASN 7 615 HIS 7 620 HIS ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 60369 Z= 0.231 Angle : 0.562 6.694 81868 Z= 0.307 Chirality : 0.040 0.172 9343 Planarity : 0.004 0.061 10259 Dihedral : 11.090 157.016 8620 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 1.89 % Allowed : 12.10 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 7117 helix: 1.03 (0.09), residues: 3169 sheet: -0.71 (0.14), residues: 1239 loop : -0.60 (0.12), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 5 343 HIS 0.006 0.001 HIS E 382 PHE 0.019 0.001 PHE X 293 TYR 0.020 0.001 TYR H 922 ARG 0.006 0.000 ARG 7 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 623 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 501 time to evaluate : 7.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 416 ASP cc_start: 0.7564 (t0) cc_final: 0.7210 (t0) REVERT: 2 809 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5908 (t-90) REVERT: 3 183 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6904 (tm-30) REVERT: 4 818 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: 5 186 CYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6785 (p) REVERT: 5 465 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6210 (mm-30) REVERT: 5 689 MET cc_start: 0.7317 (mmm) cc_final: 0.6712 (mmm) REVERT: 7 717 LEU cc_start: 0.8749 (tt) cc_final: 0.8502 (tp) REVERT: A 62 MET cc_start: 0.5830 (ppp) cc_final: 0.5623 (ppp) REVERT: C 3 TYR cc_start: 0.8700 (t80) cc_final: 0.8280 (t80) REVERT: C 119 GLU cc_start: 0.7933 (pm20) cc_final: 0.7666 (pm20) REVERT: C 170 GLU cc_start: 0.6459 (mt-10) cc_final: 0.6156 (mt-10) REVERT: H 570 ILE cc_start: 0.7078 (mm) cc_final: 0.6861 (mm) REVERT: X 287 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8253 (tp) REVERT: X 345 MET cc_start: 0.8445 (mmm) cc_final: 0.7967 (tmm) REVERT: X 437 PHE cc_start: 0.8355 (t80) cc_final: 0.8135 (t80) outliers start: 122 outliers final: 91 residues processed: 592 average time/residue: 1.3229 time to fit residues: 1323.6213 Evaluate side-chains 568 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 472 time to evaluate : 6.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 384 ASN Chi-restraints excluded: chain 2 residue 596 LEU Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 701 ASP Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 809 HIS Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 284 ASP Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 478 MET Chi-restraints excluded: chain 3 residue 653 ILE Chi-restraints excluded: chain 4 residue 217 ASN Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 321 ASP Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 704 LEU Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 4 residue 828 LEU Chi-restraints excluded: chain 5 residue 41 ASP Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 465 GLU Chi-restraints excluded: chain 5 residue 538 ASP Chi-restraints excluded: chain 5 residue 637 GLU Chi-restraints excluded: chain 6 residue 393 ASP Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 533 ILE Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 6 residue 736 MET Chi-restraints excluded: chain 6 residue 801 GLU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 20 GLU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 210 ASN Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 289 CYS Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 571 TYR Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain F residue 510 GLN Chi-restraints excluded: chain F residue 737 THR Chi-restraints excluded: chain F residue 774 MET Chi-restraints excluded: chain G residue 495 THR Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 696 CYS Chi-restraints excluded: chain G residue 739 ASP Chi-restraints excluded: chain G residue 837 LEU Chi-restraints excluded: chain G residue 848 TYR Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 592 THR Chi-restraints excluded: chain H residue 618 LEU Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain H residue 906 GLU Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain X residue 187 ILE Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 284 ILE Chi-restraints excluded: chain X residue 287 LEU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain X residue 699 ARG Chi-restraints excluded: chain X residue 702 VAL Chi-restraints excluded: chain X residue 763 LEU Chi-restraints excluded: chain Y residue 135 ASP Chi-restraints excluded: chain Y residue 139 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 234 optimal weight: 10.0000 chunk 628 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 409 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 698 optimal weight: 8.9990 chunk 579 optimal weight: 20.0000 chunk 323 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 290 HIS 4 196 ASN ** 4 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 ASN ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 576 GLN 4 848 ASN 6 409 GLN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 60369 Z= 0.278 Angle : 0.566 8.189 81868 Z= 0.310 Chirality : 0.040 0.162 9343 Planarity : 0.004 0.060 10259 Dihedral : 11.004 157.245 8620 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 1.92 % Allowed : 12.30 % Favored : 85.78 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.10), residues: 7117 helix: 1.14 (0.09), residues: 3167 sheet: -0.75 (0.14), residues: 1240 loop : -0.62 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 729 HIS 0.005 0.001 HIS E 382 PHE 0.020 0.001 PHE 4 702 TYR 0.015 0.001 TYR A 53 ARG 0.005 0.000 ARG 2 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 603 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 479 time to evaluate : 7.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 416 ASP cc_start: 0.7530 (t0) cc_final: 0.7212 (t0) REVERT: 2 809 HIS cc_start: 0.6292 (OUTLIER) cc_final: 0.5951 (t-90) REVERT: 3 308 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.5968 (mp10) REVERT: 5 465 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6247 (mm-30) REVERT: 7 717 LEU cc_start: 0.8742 (tt) cc_final: 0.8501 (tp) REVERT: A 62 MET cc_start: 0.5765 (ppp) cc_final: 0.5477 (ppp) REVERT: C 170 GLU cc_start: 0.6421 (mt-10) cc_final: 0.6156 (mt-10) REVERT: E 426 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7223 (mm-30) REVERT: G 707 LEU cc_start: 0.7738 (tp) cc_final: 0.7508 (tp) REVERT: H 570 ILE cc_start: 0.7068 (mm) cc_final: 0.6863 (mm) REVERT: X 170 MET cc_start: 0.8960 (ttm) cc_final: 0.8662 (ttt) REVERT: X 245 MET cc_start: 0.9188 (tpt) cc_final: 0.8947 (tpt) REVERT: X 287 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8239 (tp) REVERT: X 345 MET cc_start: 0.8452 (mmm) cc_final: 0.7961 (tmm) REVERT: X 437 PHE cc_start: 0.8389 (t80) cc_final: 0.8151 (t80) REVERT: Y 137 MET cc_start: 0.6755 (mtm) cc_final: 0.6440 (mtp) outliers start: 124 outliers final: 108 residues processed: 577 average time/residue: 1.2997 time to fit residues: 1278.6101 Evaluate side-chains 570 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 458 time to evaluate : 6.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 384 ASN Chi-restraints excluded: chain 2 residue 458 ARG Chi-restraints excluded: chain 2 residue 596 LEU Chi-restraints excluded: chain 2 residue 620 ILE Chi-restraints excluded: chain 2 residue 701 ASP Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 809 HIS Chi-restraints excluded: chain 2 residue 843 ASP Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 284 ASP Chi-restraints excluded: chain 3 residue 308 GLN Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 402 ASP Chi-restraints excluded: chain 3 residue 478 MET Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 321 ASP Chi-restraints excluded: chain 4 residue 580 TYR Chi-restraints excluded: chain 4 residue 591 THR Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 4 residue 828 LEU Chi-restraints excluded: chain 5 residue 41 ASP Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 278 CYS Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 409 ASP Chi-restraints excluded: chain 5 residue 465 GLU Chi-restraints excluded: chain 5 residue 538 ASP Chi-restraints excluded: chain 6 residue 393 ASP Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 533 ILE Chi-restraints excluded: chain 6 residue 683 ASN Chi-restraints excluded: chain 6 residue 736 MET Chi-restraints excluded: chain 6 residue 801 GLU Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 20 GLU Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 239 ILE Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 289 CYS Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 571 TYR Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain F residue 510 GLN Chi-restraints excluded: chain F residue 774 MET Chi-restraints excluded: chain G residue 495 THR Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 690 SER Chi-restraints excluded: chain G residue 696 CYS Chi-restraints excluded: chain G residue 739 ASP Chi-restraints excluded: chain G residue 821 MET Chi-restraints excluded: chain G residue 827 TYR Chi-restraints excluded: chain G residue 837 LEU Chi-restraints excluded: chain G residue 848 TYR Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 592 THR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 646 SER Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain H residue 747 LEU Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain H residue 906 GLU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 187 ILE Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 287 LEU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain X residue 593 GLU Chi-restraints excluded: chain X residue 699 ARG Chi-restraints excluded: chain X residue 701 PHE Chi-restraints excluded: chain X residue 702 VAL Chi-restraints excluded: chain X residue 763 LEU Chi-restraints excluded: chain Y residue 135 ASP Chi-restraints excluded: chain Y residue 139 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 673 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 398 optimal weight: 0.8980 chunk 510 optimal weight: 7.9990 chunk 395 optimal weight: 0.9980 chunk 588 optimal weight: 0.3980 chunk 390 optimal weight: 1.9990 chunk 695 optimal weight: 0.7980 chunk 435 optimal weight: 6.9990 chunk 424 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 60369 Z= 0.149 Angle : 0.519 7.230 81868 Z= 0.279 Chirality : 0.039 0.164 9343 Planarity : 0.004 0.057 10259 Dihedral : 10.791 155.792 8620 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.12 % Favored : 96.87 % Rotamer: Outliers : 1.40 % Allowed : 12.81 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 7117 helix: 1.53 (0.09), residues: 3163 sheet: -0.56 (0.14), residues: 1252 loop : -0.38 (0.12), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 5 343 HIS 0.005 0.001 HIS E 382 PHE 0.020 0.001 PHE X 293 TYR 0.015 0.001 TYR A 53 ARG 0.004 0.000 ARG 2 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 603 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 513 time to evaluate : 7.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 416 ASP cc_start: 0.7481 (t0) cc_final: 0.7119 (t0) REVERT: 2 809 HIS cc_start: 0.6161 (OUTLIER) cc_final: 0.5831 (t-90) REVERT: 5 186 CYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6729 (p) REVERT: 5 530 TYR cc_start: 0.7508 (t80) cc_final: 0.7236 (t80) REVERT: 6 613 VAL cc_start: 0.8706 (t) cc_final: 0.8498 (m) REVERT: 7 717 LEU cc_start: 0.8689 (tt) cc_final: 0.8444 (tp) REVERT: A 62 MET cc_start: 0.6040 (ppp) cc_final: 0.5770 (ppp) REVERT: C 3 TYR cc_start: 0.8667 (t80) cc_final: 0.8215 (t80) REVERT: C 170 GLU cc_start: 0.6329 (mt-10) cc_final: 0.6004 (mt-10) REVERT: C 173 GLU cc_start: 0.7796 (mt-10) cc_final: 0.6541 (mt-10) REVERT: E 426 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7130 (mm-30) REVERT: G 629 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.5550 (m-70) REVERT: X 245 MET cc_start: 0.9184 (tpt) cc_final: 0.8943 (tpt) REVERT: X 287 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8198 (tp) REVERT: X 345 MET cc_start: 0.8433 (mmm) cc_final: 0.7974 (tmm) outliers start: 90 outliers final: 71 residues processed: 583 average time/residue: 1.3283 time to fit residues: 1310.3220 Evaluate side-chains 540 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 465 time to evaluate : 6.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 458 ARG Chi-restraints excluded: chain 2 residue 596 LEU Chi-restraints excluded: chain 2 residue 701 ASP Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 809 HIS Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 284 ASP Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 828 LEU Chi-restraints excluded: chain 5 residue 41 ASP Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 278 CYS Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 610 CYS Chi-restraints excluded: chain 6 residue 393 ASP Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 669 HIS Chi-restraints excluded: chain 6 residue 736 MET Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 289 CYS Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 571 TYR Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain F residue 510 GLN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 774 MET Chi-restraints excluded: chain G residue 495 THR Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 739 ASP Chi-restraints excluded: chain G residue 837 LEU Chi-restraints excluded: chain G residue 848 TYR Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain H residue 480 SER Chi-restraints excluded: chain H residue 592 THR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 287 LEU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain X residue 593 GLU Chi-restraints excluded: chain X residue 699 ARG Chi-restraints excluded: chain X residue 702 VAL Chi-restraints excluded: chain X residue 763 LEU Chi-restraints excluded: chain Y residue 135 ASP Chi-restraints excluded: chain Y residue 139 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 430 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 415 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 442 optimal weight: 10.0000 chunk 474 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 546 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 723 HIS 6 409 GLN 7 112 HIS B 139 HIS D 58 GLN E 155 GLN E 249 ASN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 753 ASN H 563 HIS ** H 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 357 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 60369 Z= 0.407 Angle : 0.621 7.151 81868 Z= 0.340 Chirality : 0.042 0.176 9343 Planarity : 0.005 0.117 10259 Dihedral : 10.919 157.617 8620 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 1.86 % Allowed : 13.17 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 7117 helix: 1.18 (0.09), residues: 3166 sheet: -0.84 (0.14), residues: 1237 loop : -0.69 (0.12), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 729 HIS 0.008 0.001 HIS C 98 PHE 0.018 0.002 PHE X 293 TYR 0.024 0.002 TYR 7 260 ARG 0.027 0.001 ARG 6 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14234 Ramachandran restraints generated. 7117 Oldfield, 0 Emsley, 7117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 269 is missing expected H atoms. Skipping. Residue MET 781 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 923 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue THR 345 is missing expected H atoms. Skipping. Residue LYS 390 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue LYS 737 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 324 is missing expected H atoms. Skipping. Residue THR 158 is missing expected H atoms. Skipping. Residue LYS 465 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LEU 910 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Evaluate side-chains 560 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 440 time to evaluate : 6.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 416 ASP cc_start: 0.7567 (t0) cc_final: 0.7262 (t0) REVERT: 2 809 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.5957 (t-90) REVERT: 3 308 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.5930 (mp10) REVERT: 6 613 VAL cc_start: 0.8772 (t) cc_final: 0.8565 (m) REVERT: 7 717 LEU cc_start: 0.8761 (tt) cc_final: 0.8529 (tp) REVERT: A 62 MET cc_start: 0.5885 (ppp) cc_final: 0.5426 (ppp) REVERT: C 170 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6089 (mt-10) REVERT: E 426 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7357 (mm-30) REVERT: E 617 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5728 (t0) REVERT: X 170 MET cc_start: 0.8916 (ttm) cc_final: 0.8602 (ttt) REVERT: X 245 MET cc_start: 0.9249 (tpt) cc_final: 0.8966 (tpt) REVERT: X 287 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8269 (tp) REVERT: X 345 MET cc_start: 0.8454 (mmm) cc_final: 0.7935 (tmm) REVERT: X 536 PHE cc_start: 0.7856 (t80) cc_final: 0.7409 (t80) outliers start: 120 outliers final: 91 residues processed: 533 average time/residue: 1.3315 time to fit residues: 1205.5115 Evaluate side-chains 521 residues out of total 6496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 426 time to evaluate : 6.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 384 ASN Chi-restraints excluded: chain 2 residue 458 ARG Chi-restraints excluded: chain 2 residue 596 LEU Chi-restraints excluded: chain 2 residue 701 ASP Chi-restraints excluded: chain 2 residue 779 HIS Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 809 HIS Chi-restraints excluded: chain 3 residue 18 ASP Chi-restraints excluded: chain 3 residue 227 THR Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 284 ASP Chi-restraints excluded: chain 3 residue 308 GLN Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 478 MET Chi-restraints excluded: chain 3 residue 558 ASP Chi-restraints excluded: chain 4 residue 294 ASP Chi-restraints excluded: chain 4 residue 321 ASP Chi-restraints excluded: chain 4 residue 723 HIS Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 4 residue 828 LEU Chi-restraints excluded: chain 5 residue 41 ASP Chi-restraints excluded: chain 5 residue 42 SER Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 186 CYS Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 278 CYS Chi-restraints excluded: chain 5 residue 279 ASP Chi-restraints excluded: chain 5 residue 409 ASP Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 538 ASP Chi-restraints excluded: chain 5 residue 637 GLU Chi-restraints excluded: chain 6 residue 158 LEU Chi-restraints excluded: chain 6 residue 343 PHE Chi-restraints excluded: chain 6 residue 393 ASP Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 548 LEU Chi-restraints excluded: chain 6 residue 736 MET Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 7 residue 289 CYS Chi-restraints excluded: chain 7 residue 459 MET Chi-restraints excluded: chain 7 residue 563 ILE Chi-restraints excluded: chain 7 residue 571 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 617 ASP Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain F residue 510 GLN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain G residue 495 THR Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 690 SER Chi-restraints excluded: chain G residue 739 ASP Chi-restraints excluded: chain G residue 821 MET Chi-restraints excluded: chain G residue 848 TYR Chi-restraints excluded: chain G residue 855 LEU Chi-restraints excluded: chain G residue 889 LEU Chi-restraints excluded: chain H residue 554 ILE Chi-restraints excluded: chain H residue 592 THR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 646 SER Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 700 SER Chi-restraints excluded: chain H residue 706 LEU Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain H residue 906 GLU Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 29 THR Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 287 LEU Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 338 LEU Chi-restraints excluded: chain X residue 370 ASP Chi-restraints excluded: chain X residue 593 GLU Chi-restraints excluded: chain X residue 699 ARG Chi-restraints excluded: chain X residue 701 PHE Chi-restraints excluded: chain X residue 702 VAL Chi-restraints excluded: chain X residue 763 LEU Chi-restraints excluded: chain Y residue 135 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 722 random chunks: chunk 633 optimal weight: 9.9990 chunk 666 optimal weight: 7.9990 chunk 608 optimal weight: 20.0000 chunk 648 optimal weight: 9.9990 chunk 390 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 509 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 585 optimal weight: 5.9990 chunk 613 optimal weight: 0.0870 chunk 646 optimal weight: 10.0000 overall best weight: 3.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: